Mercurial > repos > iuc > seurat
changeset 15:fab6ff46e019 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
| author | iuc |
|---|---|
| date | Fri, 07 Jul 2023 01:43:02 +0000 |
| parents | c0fd285eb553 |
| children | |
| files | Seurat.R citeseq_Seurat.R macros.xml seurat.xml test-data/adt.tab.gz test-data/markers.tsv test-data/protein_out.tsv test-data/rna.tab.gz test-data/rna_out.tsv |
| diffstat | 9 files changed, 2316 insertions(+), 157 deletions(-) [+] |
line wrap: on
line diff
--- a/Seurat.R Mon Nov 21 14:35:28 2022 +0000 +++ b/Seurat.R Fri Jul 07 01:43:02 2023 +0000 @@ -8,19 +8,24 @@ #' low_thresholds: "" #' high_thresholds: "" #' numPCs: "" -#' cells_use: "" #' resolution: "" #' perplexity: "" #' min_pct: "" #' logfc_threshold: "" +#' end_step: "" #' showcode: "" #' warn: "" #' varstate: "" #' vlnfeat: "" #' featplot: "" #' PCplots: "" -#' tsne: "" +#' nmds: "" #' heatmaps: "" +#' norm_out: "" +#' variable_out: "" +#' pca_out : "" +#' clusters_out: "" +#' markers_out: "" #' --- # nolint start @@ -34,87 +39,148 @@ vlnfeat <- as.logical(params$vlnfeat) featplot <- as.logical(params$featplot) pc_plots <- as.logical(params$PCplots) -tsne <- as.logical(params$tsne) +nmds <- as.logical(params$nmds) heatmaps <- as.logical(params$heatmaps) - +end_step <- as.integer(params$end_step) +norm_out <- as.logical(params$norm_out) # we need that to not crash Galaxy with an UTF-8 error on German LC settings. loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") #+ echo = F, warning = `warn`, include =`varstate` min_cells <- as.integer(params$min_cells) min_genes <- as.integer(params$min_genes) -low_thresholds <- as.integer(params$low_thresholds) -high_thresholds <- as.integer(params$high_thresholds) -num_pcs <- as.integer(params$numPCs) -cells_use <- as.integer(params$cells_use) -resolution <- as.double(params$resolution) -perplexity <- as.integer(params$perplexity) -min_pct <- as.double(params$min_pct) -logfc_threshold <- as.double(params$logfc_thresh) print(paste0("Minimum cells: ", min_cells)) print(paste0("Minimum features: ", min_genes)) +low_thresholds <- as.integer(params$low_thresholds) +high_thresholds <- as.integer(params$high_thresholds) print(paste0("Umi low threshold: ", low_thresholds)) print(paste0("Umi high threshold: ", high_thresholds)) -print(paste0("Number of principal components: ", num_pcs)) -print(paste0("Resolution: ", resolution)) -print(paste0("Perplexity: ", perplexity)) -print(paste0("Minimum percent of cells", min_pct)) -print(paste0("Logfold change threshold", logfc_threshold)) + +if (end_step >= 2) { + variable_out <- as.logical(params$variable_out) +} + -#+ echo = FALSE +if (end_step >= 3) { + num_pcs <- as.integer(params$numPCs) + print(paste0("Number of principal components: ", num_pcs)) + pca_out <- as.logical(params$pca_out) +} +if (end_step >= 4) { + if (params$perplexity == "") { + perplexity <- -1 + print(paste0("Perplexity: ", perplexity)) + } else { + perplexity <- as.integer(params$perplexity) + print(paste0("Perplexity: ", perplexity)) + } + resolution <- as.double(params$resolution) + print(paste0("Resolution: ", resolution)) + clusters_out <- as.logical(params$clusters_out) +} +if (end_step >= 5) { + min_pct <- as.double(params$min_pct) + logfc_threshold <- as.double(params$logfc_thresh) + print(paste0("Minimum percent of cells", min_pct)) + print(paste0("Logfold change threshold", logfc_threshold)) + markers_out <- as.logical(params$markers_out) +} + + if (showcode == TRUE) print("Read in data, generate inital Seurat object") #+ echo = `showcode`, warning = `warn`, message = F counts <- read.delim(params$counts, row.names = 1) seuset <- Seurat::CreateSeuratObject(counts = counts, min.cells = min_cells, min.features = min_genes) -#+ echo = FALSE if (showcode == TRUE && vlnfeat == TRUE) print("Raw data vizualization") #+ echo = `showcode`, warning = `warn`, include=`vlnfeat` -Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA")) -Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA") +if (vlnfeat == TRUE){ + print(Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA"))) + print(Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA")) +} -#+ echo = FALSE if (showcode == TRUE) print("Filter and normalize for UMI counts") #+ echo = `showcode`, warning = `warn` seuset <- subset(seuset, subset = `nCount_RNA` > low_thresholds & `nCount_RNA` < high_thresholds) seuset <- Seurat::NormalizeData(seuset, normalization.method = "LogNormalize", scale.factor = 10000) +if (norm_out == TRUE) { + saveRDS(seuset, "norm_out.rds") +} -#+ echo = FALSE -if (showcode == TRUE && featplot == TRUE) print("Variable Genes") -#+ echo = `showcode`, warning = `warn`, include = `featplot` -seuset <- Seurat::FindVariableFeatures(object = seuset, selection.method = "mvp") -Seurat::VariableFeaturePlot(seuset, cols = c("black", "red"), selection.method = "disp") -seuset <- Seurat::ScaleData(object = seuset, vars.to.regress = "nCount_RNA") +if (end_step >= 2) { + #+ echo = FALSE + if (showcode == TRUE && featplot == TRUE) print("Variable Genes") + #+ echo = `showcode`, warning = `warn`, include = `featplot` + seuset <- Seurat::FindVariableFeatures(object = seuset, selection.method = "mvp") + if (featplot == TRUE) { + print(Seurat::VariableFeaturePlot(seuset, cols = c("black", "red"), selection.method = "disp")) + } + seuset <- Seurat::ScaleData(object = seuset, vars.to.regress = "nCount_RNA") + if (variable_out == TRUE) { + saveRDS(seuset, "var_out.rds") + } +} -#+ echo = FALSE -if (showcode == TRUE && pc_plots == TRUE) print("PCA Visualization") -#+ echo = `showcode`, warning = `warn`, include = `pc_plots` -seuset <- Seurat::RunPCA(seuset, npcs = num_pcs) -Seurat::VizDimLoadings(seuset, dims = 1:2) -Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca") -Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 30, reduction = "pca") -seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100) -seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs) -Seurat::JackStrawPlot(seuset, dims = 1:num_pcs) -Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca") +if (end_step >= 3) { + #+ echo = FALSE + if (showcode == TRUE && pc_plots == TRUE) print("PCA Visualization") + #+ echo = `showcode`, warning = `warn`, include = `pc_plots` + seuset <- Seurat::RunPCA(seuset, npcs = num_pcs) + seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100) + seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs) + if (pc_plots == TRUE) { + print(Seurat::VizDimLoadings(seuset, dims = 1:2)) + print(Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca")) + print(Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 30, reduction = "pca")) + print(Seurat::JackStrawPlot(seuset, dims = 1:num_pcs)) + print(Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca")) + } + if (pca_out == TRUE) { + saveRDS(seuset, "pca_out.rds") + } +} -#+ echo = FALSE -if (showcode == TRUE && tsne == TRUE) print("tSNE") -#+ echo = `showcode`, warning = `warn`, include = `tsne` -seuset <- Seurat::FindNeighbors(object = seuset) -seuset <- Seurat::FindClusters(object = seuset) -if (perplexity == -1) { - seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution); -} else { - seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity); +if (end_step >= 4) { + #+ echo = FALSE + if (showcode == TRUE && nmds == TRUE) print("tSNE and UMAP") + #+ echo = `showcode`, warning = `warn`, include = `nmds` + seuset <- Seurat::FindNeighbors(object = seuset) + seuset <- Seurat::FindClusters(object = seuset) + if (perplexity == -1) { + seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution); + } else { + seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity); + } + if (nmds == TRUE) { + print(Seurat::DimPlot(seuset, reduction = "tsne")) + } + seuset <- Seurat::RunUMAP(seuset, dims = 1:num_pcs) + if (nmds == TRUE) { + print(Seurat::DimPlot(seuset, reduction = "umap")) + } + if (clusters_out == TRUE) { + tsnedata <- Seurat::Embeddings(seuset, reduction="tsne") + saveRDS(seuset, "tsne_out.rds") + umapdata <- Seurat::Embeddings(seuset, reduction="umap") + saveRDS(seuset, "umap_out.rds") + } } -Seurat::DimPlot(seuset, reduction = "tsne") + -#+ echo = FALSE -if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes") -#+ echo = `showcode`, warning = `warn`, include = `heatmaps` -markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold) -top10 <- dplyr::group_by(markers, cluster) -top10 <- dplyr::top_n(top10, 10, avg_log2FC) -Seurat::DoHeatmap(seuset, features = top10$gene) +if (end_step == 5) { + #+ echo = FALSE + if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes") + #+ echo = `showcode`, warning = `warn`, include = `heatmaps` + markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold) + top10 <- dplyr::group_by(markers, cluster) + top10 <- dplyr::top_n(top10, n = 10, wt = avg_log2FC) + print(top10) + if (heatmaps == TRUE) { + print(Seurat::DoHeatmap(seuset, features = top10$gene)) + } + if (markers_out == TRUE) { + saveRDS(seuset, "markers_out.rds") + data.table::fwrite(x = markers, row.names=TRUE, sep="\t", file = "markers_out.tsv") + } +} # nolint end
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/citeseq_Seurat.R Fri Jul 07 01:43:02 2023 +0000 @@ -0,0 +1,260 @@ +#' --- +#' title: "Seurat Cite-seq Analysis" +#' author: "Performed using Galaxy" +#' params: +#' rna: "" +#' prot: "" +#' min_cells: "" +#' min_genes: "" +#' low_thresholds: "" +#' high_thresholds: "" +#' numPCs: "" +#' resolution: "" +#' perplexity: "" +#' min_pct: "" +#' logfc_threshold: "" +#' showcode: "" +#' warn: "" +#' varstate: "" +#' vlnfeat: "" +#' featplot: "" +#' PCplots: "" +#' nmds: "" +#' heatmaps: "" +#' norm_out: "" +#' variable_out: "" +#' pca_out : "" +#' clusters_out: "" +#' markers_out: "" +#' cite_markers: "" +#' comparison: "" +#' feat_comp: "" +#' marker_compare: "" +#' top_x: "" +#' --- + +# nolint start +#+ echo=F, warning = F, message=F +options(show.error.messages = F, error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) +}) + +# we need that to not crash Galaxy with an UTF-8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +showcode <- as.logical(params$showcode) +warn <- as.logical(params$warn) +varstate <- as.logical(params$varstate) +vlnfeat <- as.logical(params$vlnfeat) +featplot <- as.logical(params$featplot) +pc_plots <- as.logical(params$PCplots) +nmds <- as.logical(params$nmds) +heatmaps <- as.logical(params$heatmaps) +end_step <- as.integer(params$end_step) +norm_out <- as.logical(params$norm_out) +comparison <- as.logical(params$comparison) +feature <- trimws(unlist(strsplit(as.character(params$feat_comp), ","))) +marker_compare <- as.logical(params$marker_compare) +top_x <- as.integer(params$top_x) +min_cells <- as.integer(params$min_cells) +min_genes <- as.integer(params$min_genes) +low_thresholds <- as.integer(params$low_thresholds) +high_thresholds <- as.integer(params$high_thresholds) +num_pcs <- as.integer(params$numPCs) +cells_use <- as.integer(params$cells_use) +resolution <- as.double(params$resolution) +min_pct <- as.double(params$min_pct) +logfc_threshold <- as.double(params$logfc_thresh) +variable_out <- as.logical(params$variable_out) +pca_out <- as.logical(params$pca_out) +clusters_out <- as.logical(params$clusters_out) +markers_out <- as.logical(params$markers_out) + +print(paste0("Minimum cells: ", min_cells)) +print(paste0("Minimum features: ", min_genes)) +print(paste0("Umi low threshold: ", low_thresholds)) +print(paste0("Umi high threshold: ", high_thresholds)) +print(paste0("Number of principal components: ", num_pcs)) +print(paste0("Resolution: ", resolution)) +print(paste0("Minimum percent of cells", min_pct)) +print(paste0("Logfold change threshold", logfc_threshold)) +if (params$perplexity == "") { + perplexity <- -1 + print(paste0("Perplexity: ", perplexity)) +} else { + perplexity <- as.integer(params$perplexity) + print(paste0("Perplexity: ", perplexity)) +} + +#+ echo = FALSE +if (showcode == TRUE) print("Read in data, generate inital Seurat object") +#+ echo = `showcode`, warning = `warn`, message = F +rna <- read.delim(params$rna, row.names = 1) +rna <- Seurat::CollapseSpeciesExpressionMatrix(rna) +protein <- read.delim(params$prot, row.names = 1) +tryCatch(all.equal(colnames(rna), colnames(protein)), error = "Columns do not match in input files") +seuset <- Seurat::CreateSeuratObject(counts = rna, min.cells = min_cells, min.features = min_genes) + +if (showcode == TRUE) print("asdf") +#+ echo = `showcode`, warning = `warn`, message = F +prot_obj <- Seurat::CreateAssayObject(counts = protein) + +if (showcode == TRUE) print("qwer") +#+ echo = `showcode`, warning = `warn`, message = F +seuset[["ADT"]] <- prot_obj + +if (showcode == TRUE) print("zxcv") +#+ echo = `showcode`, warning = `warn`, message = F +Seurat::DefaultAssay(seuset) <- "RNA" + +if (showcode == TRUE && vlnfeat == TRUE) print("Raw data vizualization") +#+ echo = `showcode`, warning = `warn`, include=`vlnfeat` +if (vlnfeat == TRUE){ + print(Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA"))) + print(Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA")) +} + +if (showcode == TRUE) print("Filter and normalize for UMI counts") +#+ echo = `showcode`, warning = `warn` +seuset <- subset(seuset, subset = `nCount_RNA` > low_thresholds & `nCount_RNA` < high_thresholds) +seuset <- Seurat::NormalizeData(seuset, normalization.method = "LogNormalize", scale.factor = 10000) +if (norm_out == TRUE) { + saveRDS(seuset, "norm_out.rds") +} + + +if (showcode == TRUE && featplot == TRUE) print("Variable Genes") +#+ echo = `showcode`, warning = `warn`, include = `featplot` +seuset <- Seurat::FindVariableFeatures(object = seuset, selection.method = "mvp") +if (featplot == TRUE) { + print(Seurat::VariableFeaturePlot(seuset, cols = c("black", "red"), selection.method = "disp")) +} +seuset <- Seurat::ScaleData(object = seuset, vars.to.regress = "nCount_RNA") +if (variable_out == TRUE) { + saveRDS(seuset, "var_out.rds") +} + + + +if (showcode == TRUE && pc_plots == TRUE) print("PCA Visualization") +#+ echo = `showcode`, warning = `warn`, include = `pc_plots` +seuset <- Seurat::RunPCA(seuset, npcs = num_pcs) +seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100) +seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs) +if (pc_plots == TRUE) { + print(Seurat::VizDimLoadings(seuset, dims = 1:2)) + print(Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca")) + print(Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 10, reduction = "pca")) + print(Seurat::JackStrawPlot(seuset, dims = 1:num_pcs)) + print(Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca")) +} +if (pca_out == TRUE) { + saveRDS(seuset, "pca_out.rds") +} + + + +if (showcode == TRUE && nmds == TRUE) print("tSNE and UMAP") +#+ echo = `showcode`, warning = `warn`, include = `nmds` +seuset <- Seurat::FindNeighbors(object = seuset) +seuset <- Seurat::FindClusters(object = seuset) +if (perplexity == -1) { + seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, check_duplicates = FALSE) +} else { + seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity, check_duplicates = FALSE) +} +if (nmds == TRUE) { + print(Seurat::DimPlot(seuset, reduction = "tsne")) +} +seuset <- Seurat::RunUMAP(seuset, dims = 1:num_pcs) +if (nmds == TRUE) { + print(Seurat::DimPlot(seuset, reduction = "umap")) +} +if (clusters_out == TRUE) { + tsnedata <- Seurat::Embeddings(seuset, reduction="tsne") + saveRDS(seuset, "tsne_out.rds") + umapdata <- Seurat::Embeddings(seuset, reduction="umap") + saveRDS(seuset, "umap_out.rds") +} + +if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes") +#+ echo = `showcode`, warning = `warn`, include = `heatmaps` +markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold) +top10 <- dplyr::group_by(markers, cluster) +top10 <- dplyr::top_n(top10, n = 10, wt = avg_log2FC) +print(top10) +if (heatmaps == TRUE) { + print(Seurat::DoHeatmap(seuset, features = top10$gene)) +} +if (markers_out == TRUE) { + saveRDS(seuset, "markers_out.rds") + data.table::fwrite(x = markers, row.names=TRUE, sep="\t", file = "markers_out.tsv") +} + +#+ echo = FALSE +if (showcode == TRUE && comparison == TRUE) print("Compare") +#+ echo = `showcode`, warning = `warn`, include = `comparison` + Seurat::DefaultAssay(seuset) <- "ADT" + seuset <- Seurat::NormalizeData(seuset, normalization.method = "CLR", margin = 2) + Seurat::DefaultAssay(seuset) <- "RNA" + seuset <- Seurat::NormalizeData(seuset, normalization.method = "CLR", margin = 2, assay = "ADT") +if (comparison == TRUE) { + for(x in feature) { + Seurat::DefaultAssay(seuset) <- "ADT" + p1 <- Seurat::FeaturePlot(seuset, x, cols = c("lightgrey", "red")) + ggplot2::ggtitle(paste0("Protein:", " ", x)) + Seurat::DefaultAssay(seuset) <- "RNA" + p2 <- Seurat::FeaturePlot(seuset, x) + ggplot2::ggtitle(paste0("RNA:", " ", x)) + print(p1 | p2) + label <- as.character(paste0(Seurat::Key(seuset[["ADT"]]), x)) + print(Seurat::VlnPlot(seuset, paste0("rna_", x))) + print(Seurat::VlnPlot(seuset, paste0("adt_", x))) + } +} + +#+ echo = FALSE +if (showcode == TRUE) print("Cite-seq") +#+ echo = `showcode`, warning = `warn`, include = `marker_compare` +rna_markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold, assay="RNA") +protein_markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold, assay="ADT") +if (marker_compare == TRUE) { + data.table::fwrite(x = rna_markers, sep="\t", file = "rna_out.tsv") + data.table::fwrite(x = protein_markers, sep="\t", file = "protein_out.tsv") +} +toprna <- dplyr::top_n(dplyr::group_by(rna_markers, cluster), n=5, avg_log2FC) +toprna <- head(as.list(unique(as.data.frame(toprna)$gene)), top_x) +topprot <- dplyr::top_n(dplyr::group_by(protein_markers, cluster), n=5, avg_log2FC) +topprot <- head(as.list(unique(as.data.frame(topprot)$gene)), top_x) +if(marker_compare == TRUE) { + pdf(file="citeseq_out.pdf") + rna_labels <- as.vector(toprna) + rna_labels <- rna_labels[!duplicated(rna_labels)] + prot_labels <- as.vector(topprot) + prot_labels <- prot_labels[!duplicated(prot_labels)] + for(rnamarker in rna_labels) { + rnamarker <- paste("rna_", rnamarker, sep = "") + for(protmarker in prot_labels) { + protmarker <- paste("adt_", protmarker, sep="") + plot <- Seurat::FeatureScatter(seuset, feature1 = rnamarker, feature2 = protmarker) + ggplot2::ggtitle(paste0(rnamarker, " vs ", protmarker)) + print(plot) + } + } + for(rnamarker in rna_labels) { + rnamarker <- paste("rna_", rnamarker, sep = "") + for(rnamarker2 in rna_labels) { + rnamarker2 <- paste("rna_", rnamarker2, sep="") + plot <- Seurat::FeatureScatter(seuset, feature1 = rnamarker, feature2 = rnamarker2) + ggplot2::ggtitle(paste0(rnamarker, " vs ", rnamarker2)) + print(plot) + } + } + for(protmarker in prot_labels) { + protmarker <- paste("adt_", protmarker, sep = "") + for(protmarker2 in prot_labels) { + protmarker2 <- paste("adt_", protmarker2, sep="") + plot <- Seurat::FeatureScatter(seuset, feature1 = protmarker, feature2 = protmarker2) + ggplot2::ggtitle(paste0(protmarker, " vs ", protmarker2)) + print(plot) + } + } + dev.off() +} + +# nolint end
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 07 01:43:02 2023 +0000 @@ -0,0 +1,67 @@ +<macros> + <token name="@TOOL_VERSION@">4.3.0.1</token> + <token name="@FUNCTION_BASE@">function['function_select'] == "base"</token> + <token name="@FUNCTION_CITE@">function['function_select'] == "cite"</token> + <token name="@VARIABLE_CONTINUE@">function['variable_continue']['variable_continue'] == "yes"</token> + <token name="@PCA_CONTINUE@">function['variable_continue']['pca_continue']['pca_continue'] == "yes"</token> + <token name="@CLUSTERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['clusters_continue'] == "yes"</token> + <token name="@MARKERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_continue'] == "yes"</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement> + <requirement type="package" version="2.22">r-rmarkdown</requirement> + <requirement type="package" version="1.14.2">r-data.table</requirement> + </requirements> + </xml> + <xml name="norm" label="Normalizing data" expanded="true"> + <param name="low_thresholds" type="integer" value="1" min="0" label="Low threshold for filtering cells" /> + <param name="high_thresholds" type="integer" value="20000000" min="1" label="High threshold for filtering cells" /> + <param name="vlnfeat" type="boolean" truevalue="T" falsevalue="F" label="Include violin plot and scatter plot of cell features"/> + <param name="norm_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data normalization"/> + </xml> + <xml name="variable" label="Variable features" expanded="true"> + <param name="featplot" type="boolean" truevalue="T" falsevalue="F" label="Include plot of variable features"/> + <param name="var_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data scaling"/> + </xml> + <xml name="pca" label="Principal component analysis" expanded="true"> + <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" /> + <param name="pc_plots" type="boolean" truevalue="T" falsevalue="F" label="Include PCA plots"/> + <param name="pca_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after PCA analysis"/> + </xml> + <xml name="clusters" label="Multidimensional scaling and Clustering" expanded="true"> + <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" min="1"/> + <param name="resolution" type="float" value="0.6" min="0" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" /> + <param name="nmds" type="boolean" truevalue="T" falsevalue="F" label="Include UMAP and TSNE plots"/> + <param name="clusters_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after TSNE and UMAP analysis"/> + </xml> + <xml name="markers" label="Marker genes" expanded="true"> + <param name="min_pct" type="float" value="0.1" min="0" max="1.0" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" /> + <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold" + help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" /> + <param name="heatmaps" type="boolean" truevalue="T" falsevalue="F" label="Include heatmaps of markers"/> + <param name="markers_file" type="boolean" truevalue="T" falsevalue="F" label="Output marker data"/> + </xml> + <xml name="cite-seq" label="Cite-seq analysis" expanded="true"> + <param name="cite_markers" type="boolean" truevalue="T" falsevalue="F" label="Output list of cite-seq markers"/> + <conditional name="comparison"> + <param name="comparison" type="select" label="Compare specific feature's effect on protein and rna expression?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="feat_comp" type="text" label="Feature(s) to inspect" help="Comma-separated list of features to directly compare with protein and RNA expression"/> + </when> + <when value="no"/> + </conditional> + <conditional name="marker_compare"> + <param name="marker_compare" type="select" label="Compare top RNA and protein features graphically against themselves and one another"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="top_x" type="integer" min="1" value="5" label="How many of the top features should be shown"/> + </when> + <when value="no"/> + </conditional> + </xml> +</macros> \ No newline at end of file
--- a/seurat.xml Mon Nov 21 14:35:28 2022 +0000 +++ b/seurat.xml Fri Jul 07 01:43:02 2023 +0000 @@ -1,119 +1,322 @@ -<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0"> +<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1"> <description>- toolkit for exploration of single-cell RNA-seq data</description> <macros> - <token name="@TOOL_VERSION@">4.3.0</token> + <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement> - <requirement type="package" version="2.18">r-rmarkdown</requirement> - </requirements> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -#if "vln" in $meta.plots: - #set $vln = 'T' -#else - #set $vln = 'F' -#end if -#if "feat" in $meta.plots: - #set $feat = 'T' -#else - #set $feat = 'F' -#end if -#if "PCs" in $meta.plots: - #set $PCs = 'T' -#else - #set $PCs = 'F' -#end if -#if "tsne" in $meta.plots: - #set $tsne = 'T' -#else - #set $tsne = 'F' -#end if -#if "heat" in $meta.plots: - #set $heatmaps = 'T' -#else - #set $heatmaps = 'F' -#end if -#if not str($adv.perplexity): - #set $adv_perplexity = -1 -#else: - #set $adv_perplexity = $adv.perplexity -#end if -Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", - params = list(counts = \"${counts}\", - min_cells = \"${adv.min_cells}\", - min_genes = \"${adv.min_genes}\", - low_thresholds = \"${adv.low_thresholds}\", - high_thresholds = \"${adv.high_thresholds}\", - numPCs = \"${adv.num_PCs}\", - cells_use = \"${adv.cells_use}\", - resolution = \"${adv.resolution}\", - perplexity = \"${adv_perplexity}\", - min_pct = \"${adv.min_pct}\", - logfc_threshold = \"${adv.logfc_threshold}\", + #if $function.function_select == "base": + Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", + params = list(counts = \"${function.input}\", + min_cells = \"${function.min_cells}\", + min_genes = \"${function.min_genes}\", + low_thresholds = \"${function.low_thresholds}\", + high_thresholds = \"${function.high_thresholds}\", + vlnfeat = \"${function.vlnfeat}\", + norm_out = \"${function.norm_file}\", + #if $function.variable_continue.variable_continue == "yes": + featplot = \"${function.variable_continue.featplot}\", + variable_out = \"${function.variable_continue.var_file}\", + #if $function.variable_continue.pca_continue.pca_continue == "yes": + numPCs = \"${function.variable_continue.pca_continue.num_PCs}\", + PCplots = \"${function.variable_continue.pca_continue.pc_plots}\", + pca_out = \"${function.variable_continue.pca_continue.pca_file}\", + #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes": + perplexity = \"${function.variable_continue.pca_continue.clusters_continue.perplexity}\", + resolution = \"${function.variable_continue.pca_continue.clusters_continue.resolution}\", + nmds = \"${function.variable_continue.pca_continue.clusters_continue.nmds}\", + clusters_out = \"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\", + #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes": + min_pct = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\", + logfc_threshold = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\", + heatmaps = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\", + markers_out = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_file}\", + end_step="\"5"\", + #else: + end_step="\"4"\", + #end if + #else: + end_step="\"3"\", + #end if + #else: + end_step="\"2"\", + #end if + #else: + end_step="\"1"\", + #end if + varstate = \"${meta.varstate}\", warn = \"${meta.warn}\", + showcode = \"${meta.showcode}\"), + intermediates_dir = \".\", + output_format = html_document(), + output_dir = \".\", + output_file = \"out.html\")" + #else: + Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/citeseq_Seurat.R\", + params = list(rna = \"${function.rna}\", + prot = \"${function.prot}\", + cite_markers = \"${function.cite_markers}\", + + + #if $function.comparison.comparison == "yes" + comparison="\"T"\", + feat_comp=\"${function.comparison.feat_comp}\", + #else: + comparison="\"F"\", + feat_comp="\""\", + #end if + #if $function.marker_compare.marker_compare == "yes" + marker_compare="\"T"\", + top_x=\"${function.marker_compare.top_x}\", + #else: + marker_compare="\"F"\", + top_x="\""\", + #end if + min_cells = \"${function.min_cells}\", + min_genes = \"${function.min_genes}\", + low_thresholds = \"${function.low_thresholds}\", + high_thresholds = \"${function.high_thresholds}\", + vlnfeat = \"${function.vlnfeat}\", + norm_out = \"${function.norm_file}\", + featplot = \"${function.featplot}\", + variable_out = \"${function.var_file}\", + numPCs = \"${function.num_PCs}\", + PCplots = \"${function.pc_plots}\", + pca_out = \"${function.pca_file}\", + perplexity = \"${function.perplexity}\", + resolution = \"${function.resolution}\", + nmds = \"${function.nmds}\", + clusters_out = \"${function.clusters_file}\", + min_pct = \"${function.min_pct}\", + logfc_threshold = \"${function.logfc_threshold}\", + heatmaps = \"${function.heatmaps}\", + markers_out = \"${function.markers_file}\", varstate = \"${meta.varstate}\", - showcode = \"${meta.showcode}\", - vlnfeat = \"$vln\", - featplot = \"$feat\", - PCplots = \"$PCs\", - tsne = \"$tsne\", - heatmaps = \"$heatmaps\"), - intermediates_dir = \".\", - output_format = html_document(), - output_dir = \".\", - output_file = \"out.html\")" + warn = \"${meta.warn}\", + showcode = \"${meta.showcode}\"), + intermediates_dir = \".\", + output_format = html_document(), + output_dir = \".\", + output_file = \"out.html\")" + #end if ]]></command> <inputs> - <param name="counts" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> - <section name="adv" title="Advanced Options" expanded="true"> - <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" /> - <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> - <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected" /> - <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> - <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" /> - <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" /> - <param name="resolution" type="float" value="0.6" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" /> - <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" /> - <param name="min_pct" type="float" value="0.1" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" /> - <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold" - help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" /> - </section> + <conditional name="function"> + <param name="function_select" type="select" label="Which Seurat method should be run?"> + <option value="base">Base</option> + <option value="cite">Cite-seq</option> + </param> + <when value="base"> + <param name="input" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> + <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> + <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/> + <expand macro="norm"/> + <conditional name="variable_continue"> + <param name="variable_continue" type="select" label="Continue workflow after Normalization step?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="variable"/> + <conditional name="pca_continue"> + <param name="pca_continue" type="select" label="Continue workflow after scaling step?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="pca"/> + <conditional name="clusters_continue"> + <param name="clusters_continue" type="select" label="Continue workflow after PCA step?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="clusters"/> + <conditional name="markers_continue"> + <param name="markers_continue" type="select" label="Continue workflow after TSNE and UMAP step?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <expand macro="markers"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="no"/> + </conditional> + </when> + <when value="no"/> + </conditional> + </when> + <when value="no"/> + </conditional> + </when> + <when value="cite"> + <param name="rna" type="data" format="tabular,tsv" label="RNA counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> + <param name="prot" type="data" format="tabular,tsv" label="Protein counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> + <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> + <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/> + <expand macro="norm"/> + <expand macro="variable"/> + <expand macro="pca"/> + <expand macro="clusters"/> + <expand macro="markers"/> + <expand macro="cite-seq"/> + </when> + </conditional> <section name="meta" title="Output options" expanded="true"> <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/> <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/> <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/> - <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?"> - <option value="vln" selected="true">Violin and Scatter plots</option> - <option value="feat" selected="true">Feature counts plots</option> - <option value="PCs" selected="true">PC plots</option> - <option value="tsne" selected="true">tSNE plots</option> - <option value="heat" selected="true">Heatmap plots</option> - </param> </section> </inputs> <outputs> <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" /> + <data name="norm_out" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} on ${on_string}: normalization intermediate output"> + <filter>@FUNCTION_BASE@</filter> + <filter>function['norm_file']</filter> + </data> + <data name="var_out" format="rdata" from_work_dir="var_out.rds" label="${tool.name} on ${on_string}: normalization and scaling intermediate output"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>function['variable_continue']['var_file']</filter> + </data> + <data name="pca_out" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} on ${on_string}: PCA embedding data"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>@PCA_CONTINUE@</filter> + <filter>function['variable_continue']['pca_continue']['pca_file']</filter> + </data> + <data name="cluters_out" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} on ${on_string}: TSNE embedding data"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>@PCA_CONTINUE@</filter> + <filter>@CLUSTERS_CONTINUE@</filter> + <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter> + </data> + <data name="umap_out" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} on ${on_string}: UMAP embedding data"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>@PCA_CONTINUE@</filter> + <filter>@CLUSTERS_CONTINUE@</filter> + <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter> + </data> + <data name="markers_out" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} on ${on_string}: Markers data"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>@PCA_CONTINUE@</filter> + <filter>@CLUSTERS_CONTINUE@</filter> + <filter>@MARKERS_CONTINUE@</filter> + <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter> + </data> + <data name="markers_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} on ${on_string}: Markers list"> + <filter>@FUNCTION_BASE@</filter> + <filter>@VARIABLE_CONTINUE@</filter> + <filter>@PCA_CONTINUE@</filter> + <filter>@CLUSTERS_CONTINUE@</filter> + <filter>@MARKERS_CONTINUE@</filter> + <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter> + <actions> + <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> + <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> + </actions> + </data> + <!-- cite-seq out --> + <data name="protmarkerst" format="tabular" from_work_dir="protein_out.tsv" label="${tool.name} cite-seq on ${on_string}: Protein markers"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['cite_markers']</filter> + <actions> + <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> + <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> + </actions> + </data> + <data name="rnamarkerst" format="tabular" from_work_dir="rna_out.tsv" label="${tool.name} cite-seq on ${on_string}: RNA markers"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['cite_markers']</filter> + <actions> + <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> + <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> + </actions> + </data> + <data name="cite_graps" format="pdf" from_work_dir="citeseq_out.pdf" label="${tool.name} cite-seq on ${on_string}: Citeseq graphs"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['marker_compare']['marker_compare'] == "yes"</filter> + </data> + <data name="norm_cite" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization intermediate output"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['norm_file']</filter> + </data> + <data name="var_cite" format="rdata" from_work_dir="var_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization and scaling intermediate output"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['var_file']</filter> + </data> + <data name="pca_cite" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} cite-seq on ${on_string}: PCA embedding data"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['pca_file']</filter> + </data> + <data name="cluters_cite" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} cite-seq on ${on_string}: TSNE embedding data"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['clusters_file']</filter> + </data> + <data name="umap_cite" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} cite-seq on ${on_string}: UMAP embedding data"> + <filter>@FUNCTION_CITE@</filter> + + <filter>function['clusters_file']</filter> + </data> + <data name="markers_cite" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} cite-seq on ${on_string}: Markers data"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['markers_file']</filter> + </data> + <data name="markers_cite_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} cite-seq on ${on_string}: Markers list"> + <filter>@FUNCTION_CITE@</filter> + <filter>function['markers_file']</filter> + <actions> + <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" /> + <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" /> + </actions> + </data> </outputs> - <tests> - <test> - <param name="counts" ftype="tabular" value="counts.tab.gz"/> - <section name="adv"> - <param name="numPCs" value="10" /> + <test expect_num_outputs="8"> + <conditional name="function"> + <param name="function_select" value="base"/> + <param name="input" ftype="tabular" value="counts.tab.gz"/> <param name="min_cells" value="3"/> <param name="min_genes" value="200"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> - <param name="cells_use" value="500"/> - <param name="resolution" value="0.6" /> - <param name="min_pct" value="0.25" /> - <param name="logfc_threshold" value="0.25" /> - </section> + <param name="vlnfeat" value="T"/> + <param name="norm_file" value="T"/> + <conditional name="variable_continue"> + <param name="variable_continue" value="yes"/> + <param name="featplot" value="T"/> + <param name="var_file" value="T"/> + <conditional name="pca_continue"> + <param name="pca_continue" value="yes"/> + <param name="numPCs" value="10" /> + <param name="pc_plots" value="T"/> + <param name="pca_file" value="T"/> + <conditional name="clusters_continue"> + <param name="clusters_continue" value="yes"/> + <param name="resolution" value="0.6" /> + <param name="nmds" value="T"/> + <param name="clusters_file" value="T"/> + <conditional name="markers_continue"> + <param name="markers_continue" value="yes"/> + <param name="min_pct" value="0.25" /> + <param name="logfc_threshold" value="0.25" /> + <param name="heatmaps" value="T"/> + <param name="markers_file" value="T"/> + </conditional> + </conditional> + </conditional> + </conditional> + </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> - <param name="plots" value="feat"/> </section> <output name="out_html" ftype="html"> <assert_contents> @@ -122,26 +325,49 @@ <has_text text="img src="data:image/png;base64" /> </assert_contents> </output> + <output name="markers_tabular" file="markers.tsv" compare="sim_size" delta="500"/> </test> - <test> <!-- perplexity test --> - <param name="counts" ftype="tabular" value="counts.tab.gz"/> - <section name="adv"> - <param name="numPCs" value="10" /> + <test expect_num_outputs="1"> + <!-- test perplexity and output filters --> + <conditional name="function"> + <param name="function_select" value="base"/> + <param name="input" ftype="tabular" value="counts.tab.gz"/> <param name="min_cells" value="3"/> <param name="min_genes" value="200"/> <param name="low_thresholds" value="1" /> <param name="high_thresholds" value="20000000" /> - <param name="cells_use" value="500"/> - <param name="resolution" value="0.6" /> - <param name="perplexity" value="16" /> - <param name="min_pct" value="0.25" /> - <param name="logfc_threshold" value="0.25" /> - </section> + <param name="vlnfeat" value="T"/> + <param name="norm_file" value="F"/> + <conditional name="variable_continue"> + <param name="variable_continue" value="yes"/> + <param name="featplot" value="T"/> + <param name="var_file" value="F"/> + <conditional name="pca_continue"> + <param name="pca_continue" value="yes"/> + <param name="numPCs" value="10" /> + <param name="pc_plots" value="T"/> + <param name="pca_file" value="F"/> + <conditional name="clusters_continue"> + <param name="clusters_continue" value="yes"/> + <param name="perplexity" value="16"/> + <param name="resolution" value="0.6" /> + <param name="nmds" value="T"/> + <param name="clusters_file" value="F"/> + <conditional name="markers_continue"> + <param name="markers_continue" value="yes"/> + <param name="min_pct" value="0.25" /> + <param name="logfc_threshold" value="0.25" /> + <param name="heatmaps" value="T"/> + <param name="markers_file" value="F"/> + </conditional> + </conditional> + </conditional> + </conditional> + </conditional> <section name="meta"> <param name="showcode" value="T"/> <param name="warn" value="F"/> <param name="varstate" value="F"/> - <param name="plots" value="feat"/> </section> <output name="out_html" ftype="html"> <assert_contents> @@ -150,6 +376,86 @@ <has_text text="img src="data:image/png;base64" /> </assert_contents> </output> + </test> + <test expect_num_outputs="4"> + <conditional name="function"> + <param name="function_select" value="cite"/> + <param name="rna" ftype="tabular" value="rna.tab.gz"/> + <param name="prot" ftype="tabular" value="adt.tab.gz"/> + <param name="min_cells" value="0"/> + <param name="min_genes" value="0"/> + <param name="low_thresholds" value="1" /> + <param name="high_thresholds" value="20000000" /> + <param name="vlnfeat" value="F"/> + <param name="norm_file" value="F"/> + <param name="featplot" value="T"/> + <param name="var_file" value="F"/> + <param name="num_PCs" value="20" /> + <param name="pc_plots" value="T"/> + <param name="pca_file" value="F"/> + <param name="resolution" value="0.6" /> + <param name="nmds" value="F"/> + <param name="clusters_file" value="F"/> + <param name="min_pct" value="0.25" /> + <param name="logfc_threshold" value="0.25" /> + <param name="heatmaps" value="T"/> + <param name="markers_file" value="F"/> + <param name="cite_markers" value="T"/> + <conditional name="comparison"> + <param name="comparison" value="yes"/> + <param name="feat_comp" value="CD4,CD19"/> + </conditional> + <conditional name="marker_compare"> + <param name="marker_compare" value="yes"/> + <param name="top_x" value="3"/> + </conditional> + </conditional> + <section name="meta"> + <param name="showcode" value="T"/> + <param name="warn" value="F"/> + <param name="varstate" value="F"/> + </section> + <output name="rnamarkerst" ftype="tabular" file="rna_out.tsv" compare="sim_size" delta="500" /> + <output name="protmarkerst" ftype="tabular" file="protein_out.tsv" compare="sim_size" delta="500" /> + </test> + <test expect_num_outputs="9"> + <conditional name="function"> + <param name="function_select" value="cite"/> + <param name="rna" ftype="tabular" value="rna.tab.gz"/> + <param name="prot" ftype="tabular" value="adt.tab.gz"/> + <param name="min_cells" value="0"/> + <param name="min_genes" value="0"/> + <param name="low_thresholds" value="1" /> + <param name="high_thresholds" value="20000000" /> + <param name="vlnfeat" value="F"/> + <param name="norm_file" value="T"/> + <param name="featplot" value="T"/> + <param name="var_file" value="T"/> + <param name="num_PCs" value="20" /> + <param name="pc_plots" value="T"/> + <param name="pca_file" value="T"/> + <param name="resolution" value="0.6" /> + <param name="nmds" value="T"/> + <param name="clusters_file" value="T"/> + <param name="min_pct" value="0.25" /> + <param name="logfc_threshold" value="0.25" /> + <param name="heatmaps" value="T"/> + <param name="markers_file" value="T"/> + <param name="cite_markers" value="F"/> + <conditional name="comparison"> + <param name="comparison" value="yes"/> + <param name="feat_comp" value="CD4,CD19"/> + </conditional> + <conditional name="marker_compare"> + <param name="marker_compare" value="yes"/> + <param name="top_x" value="3"/> + </conditional> + </conditional> + <section name="meta"> + <param name="showcode" value="T"/> + <param name="warn" value="F"/> + <param name="varstate" value="F"/> + </section> </test> </tests> <help><![CDATA[ @@ -167,6 +473,8 @@ **Inputs** * Gene count matrix in TAB-separated format + or + * RNA and Protein count matrices in TAB-separated formats -----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markers.tsv Fri Jul 07 01:43:02 2023 +0000 @@ -0,0 +1,773 @@ +"" p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene +Nucks1 1.18411323850772e-16 1.00561994844169 1 1 1.09767297209666e-13 0 Nucks1 +Gpi1 1.79982790200504e-16 1.4397713415714 1 0.975 1.66844046515867e-13 0 Gpi1 +Trp53 4.43575005074525e-16 1.67570868184123 0.986 0.949 4.11194029704085e-13 0 Trp53 +Gdf3 6.15314650265127e-15 1.75957711466652 0.944 0.802 5.70396680795773e-12 0 Gdf3 +Rpl4 9.94148370705165e-15 0.555534334164376 1 1 9.21575539643688e-12 0 Rpl4 +Ralb 1.5603785645578e-14 1.92721605141292 0.93 0.695 1.44647092934508e-11 0 Ralb +Ftl1 5.38929343854758e-14 0.896518520873592 1 1 4.99587501753361e-11 0 Ftl1 +Zfp704 3.48560933499829e-13 1.54864588651405 0.972 0.838 3.23115985354342e-10 0 Zfp704 +Tns1 5.77529013908346e-13 1.68280690355749 0.887 0.503 5.35369395893037e-10 0 Tns1 +Gcat 3.87561669839796e-12 1.69793512322551 0.958 0.807 3.59269667941491e-09 0 Gcat +St3gal4 6.49102709874417e-12 1.10146192261782 0.606 0.173 6.01718212053585e-09 0 St3gal4 +Gpa33 1.33561520892938e-11 2.12256764711496 0.592 0.208 1.23811529867753e-08 0 Gpa33 +Xrn2 3.29473696699025e-11 0.770133884184816 1 0.995 3.05422116839996e-08 0 Xrn2 +Mrpl17 3.50012211643864e-11 0.746796177121439 1 0.99 3.24461320193862e-08 0 Mrpl17 +Ceacam2 5.36266305938498e-11 0.659994093618872 0.761 0.345 4.97118865604987e-08 0 Ceacam2 +Adi1 5.64090996263144e-11 1.48358282742796 0.972 0.888 5.22912353535935e-08 0 Adi1 +Sept2 7.01918447074417e-11 0.868969458163974 1 1 6.50678400437984e-08 0 Sept2 +Ppp1r11 7.44523196438785e-11 0.918592139758593 1 0.959 6.90173003098754e-08 0 Ppp1r11 +Eif4e2 2.22092667324463e-10 0.824779756130801 1 0.995 2.05879902609777e-07 0 Eif4e2 +Cacybp 2.68829218185697e-10 1.00228344950431 0.986 0.995 2.49204685258141e-07 0 Cacybp +Eno1 6.96987523876623e-10 0.40016030945526 0.93 0.599 6.4610743463363e-07 0 Eno1 +Myeov2 1.9990246379103e-09 0.685539965183034 0.986 0.985 1.85309583934285e-06 0 Myeov2 +Gng10 3.94623730908105e-09 1.17130525771998 0.859 0.457 3.65816198551814e-06 0 Gng10 +Cd109 4.39844362440024e-09 1.91175145685468 0.408 0.107 4.07735723981902e-06 0 Cd109 +Hnrnpa0 1.58290267057998e-08 0.811216726627202 0.986 0.98 1.46735077562765e-05 0 Hnrnpa0 +Msrb2 5.48032890646332e-08 1.24147534501256 0.732 0.381 5.08026489629149e-05 0 Msrb2 +Ptcd3 6.19767456859678e-08 0.800091440706327 1 0.99 5.74524432508921e-05 0 Ptcd3 +Rai14 8.40068444688735e-08 1.31175247785821 0.845 0.538 7.78743448226457e-05 0 Rai14 +Hint2 2.26929636291787e-07 0.715455167813889 0.859 0.497 0.000210363772842486 0 Hint2 +Sra1 2.68967121984332e-07 0.93977408723431 0.972 0.924 0.000249332522079476 0 Sra1 +Fth1 1.19897530626167e-06 0.631968616609468 1 1 0.00111145010890457 0 Fth1 +2810432D09Rik 1.3935121021676e-06 1.08796030099265 0.93 0.782 0.00129178571870937 0 2810432D09Rik +Cycs 1.65526495315875e-06 0.480425114297169 1 0.995 0.00153443061157816 0 Cycs +Npr1 1.91352582651328e-06 0.832258895946477 0.972 0.766 0.00177383844117781 0 Npr1 +Oas1a 2.40234815360308e-06 1.18028761558635 0.817 0.66 0.00222697673839006 0 Oas1a +Fancm 2.50675446923527e-06 0.894104496016523 1 0.99 0.0023237613929811 0 Fancm +Pnpla6 2.84941771941601e-06 1.15711866758003 0.958 0.929 0.00264141022589864 0 Pnpla6 +Fkbp2 3.35210087424692e-06 0.681209438799815 0.958 0.909 0.00310739751042689 0 Fkbp2 +Egfl7 3.83761020774903e-06 1.06164633323232 0.732 0.467 0.00355746466258335 0 Egfl7 +Ctnnb1 4.95946741674435e-06 0.468455673768554 1 0.99 0.00459742629532201 0 Ctnnb1 +Amdhd2 5.51993168968458e-06 1.07601984805959 0.901 0.822 0.0051169766763376 0 Amdhd2 +Il1f9 6.41757293244151e-06 0.496713211958332 0.394 0.67 0.00594909010837328 0 Il1f9 +Mrpl51 7.56282674299504e-06 0.506391556742938 1 0.995 0.0070107403907564 0 Mrpl51 +Exosc8 1.06283094770493e-05 0.502095828075973 1 1 0.00985244288522468 0 Exosc8 +Prelid1 1.43265849490701e-05 0.491961820886089 0.986 0.995 0.0132807442477879 0 Prelid1 +Gabra1 2.67122398852359e-05 1.43236925093549 0.268 0.081 0.0247622463736137 0 Gabra1 +Mbtps1 2.72739402167582e-05 0.870461714008831 0.972 0.964 0.0252829425809348 0 Mbtps1 +Mov10 3.34079654469243e-05 1.21696367844458 0.915 0.863 0.0309691839692988 0 Mov10 +Acp5 3.65049797793852e-05 1.04760983011 0.915 0.812 0.0338401162554901 0 Acp5 +Chchd7 4.51309831496194e-05 1.02081770184916 0.746 0.589 0.0418364213796971 0 Chchd7 +Gpx3 5.70379877528702e-05 1.26085029503603 0.521 0.279 0.0528742146469107 0 Gpx3 +Haus8 6.65899526087587e-05 0.836817918393063 0.972 0.939 0.0617288860683193 0 Haus8 +Nemf 7.18694565946676e-05 0.63821100284542 0.986 1 0.0666229862632569 0 Nemf +Gtf2e2 7.91598779949351e-05 0.648624561426916 0.958 0.959 0.0733812069013049 0 Gtf2e2 +Sec61a2 8.99949185362504e-05 0.903614277352713 0.831 0.64 0.0834252894831041 0 Sec61a2 +Herpud1 9.27848522706712e-05 1.00590823357362 0.521 0.279 0.0860115580549122 0 Herpud1 +Ift46 0.000101108593016252 0.89362347720875 0.901 0.868 0.0937276657260654 0 Ift46 +Trip6 0.000103190741114863 0.480829502585925 0.338 0.132 0.0956578170134776 0 Trip6 +Serpine2 0.000107092595644278 1.03907303461423 0.859 0.746 0.0992748361622459 0 Serpine2 +Pus10 0.000109730993051195 1.15403503199561 0.873 0.69 0.101720630558457 0 Pus10 +Mea1 0.000111250413960631 0.432850783796133 0.986 0.99 0.103129133741505 0 Mea1 +Rpl36 0.000112067997539825 0.461259801056781 1 0.99 0.103887033719417 0 Rpl36 +Atp6v1c1 0.000112890689616442 0.533666743097121 0.986 1 0.104649669274442 0 Atp6v1c1 +Cox7a2l 0.000124562457355553 0.478030693189566 0.986 0.985 0.115469397968598 0 Cox7a2l +Synj2bp 0.000142894320641149 0.971219596035958 0.915 0.827 0.132463035234345 0 Synj2bp +Rpl37a 0.000169193073847184 0.398748711615994 1 1 0.15684197945634 0 Rpl37a +Abhd11 0.000197812724047611 0.5547907670421 0.972 0.98 0.183372395192136 0 Abhd11 +Adrb3 0.000199692414804039 0.531069650403229 0.493 0.259 0.185114868523345 0 Adrb3 +Rtn4 0.000219899720590172 0.351418508859155 1 1 0.203847040987089 0 Rtn4 +Mrpl45 0.000234225672641445 0.461706276684107 1 0.98 0.217127198538619 0 Mrpl45 +Snhg6 0.000237487747585118 0.383194718574103 1 0.959 0.220151142011405 0 Snhg6 +Cpped1 0.000315573826200206 0.696959431154922 0.775 0.528 0.292536936887591 0 Cpped1 +Casp7 0.000361313835082184 0.746827591916447 0.69 0.447 0.334937925121184 0 Casp7 +Lace1 0.000376219322631167 0.90235389508979 0.479 0.274 0.348755312079092 0 Lace1 +0610010K14Rik 0.000467796779271384 0.503834798365873 0.972 0.985 0.433647614384573 0 0610010K14Rik +Hells 0.000469351282641038 0.658064731267181 0.986 0.975 0.435088639008243 0 Hells +Pdia4 0.00051023973172748 0.788957487266592 1 0.99 0.472992231311374 0 Pdia4 +Sap18 0.000638751599987711 0.760199026880684 0.972 1 0.592122733188609 0 Sap18 +Srrt 0.0006514057506608 0.485785864588046 1 0.975 0.603853130862562 0 Srrt +Mtpn 0.00068639312380355 0.548224085459587 1 0.995 0.636286425765891 0 Mtpn +Tbrg1 0.000935512642066262 0.37794210191983 1 0.995 0.867220219195425 0 Tbrg1 +Mtdh 0.000990671497996262 0.500084727712879 1 0.99 0.918352478642535 0 Mtdh +Irak4 0.00104153448317494 1.14159374584292 0.521 0.32 0.965502465903171 0 Irak4 +Gstm6 0.00106123770302869 1.4089272734481 0.493 0.32 0.983767350707595 0 Gstm6 +Comt 0.00126628629990873 0.648345027619155 1 1 1 0 Comt +Gcdh 0.00139155863805091 1.12386350039453 0.887 0.909 1 0 Gcdh +Zdhhc6 0.00163619928497125 0.69104229446098 0.944 0.909 1 0 Zdhhc6 +Eif1a 0.00165112998117775 0.384879572301459 1 0.995 1 0 Eif1a +2310009B15Rik 0.00173210028665594 0.4248888705276 0.352 0.188 1 0 2310009B15Rik +Cyp4f13 0.00175523121640267 0.780178880617658 0.31 0.147 1 0 Cyp4f13 +Fbxo6 0.00206731020161479 0.550596980561993 0.958 0.914 1 0 Fbxo6 +Tmem180 0.00219825544955122 0.441289904734916 0.648 0.477 1 0 Tmem180 +Rpl36al 0.00228626213692379 0.269785234716447 1 1 1 0 Rpl36al +Zcchc8 0.00229294233981456 0.477022546043472 0.986 0.975 1 0 Zcchc8 +Rbbp4 0.00306653381333978 0.365498784564788 1 1 1 0 Rbbp4 +Fam172a 0.00354785319103804 0.725125734043794 0.789 0.665 1 0 Fam172a +Tmem208 0.00485111104024679 0.370686071000385 0.972 0.919 1 0 Tmem208 +Rnaseh2b 0.00531817478993866 0.490741013841635 0.944 0.893 1 0 Rnaseh2b +Laptm4a 0.00678134610491405 0.496367307461378 0.986 0.99 1 0 Laptm4a +Nop16 0.00696457086591746 0.277944801017761 1 0.949 1 0 Nop16 +Ncam1 0.00859319981088654 1.4142481569529 0.394 0.299 1 0 Ncam1 +Calu 0.00865850337374608 0.430300749669148 0.986 0.98 1 0 Calu +Reep3 0.00897789893218976 0.592508357835259 0.887 0.848 1 0 Reep3 +Larp4 1.99355266798699e-28 2.16904829192904 1 0.985 1.84802332322394e-25 1 Larp4 +Pabpc4 1.07031988904245e-25 1.23340361858578 1 0.995 9.92186537142354e-23 1 Pabpc4 +Timm17a 2.48810160017051e-25 1.11983585587203 1 0.995 2.30647018335806e-22 1 Timm17a +Hsp90aa1 1.13473528803483e-24 0.90892218384017 1 1 1.05189961200829e-21 1 Hsp90aa1 +Gldc 1.1788625663322e-19 1.45309001864455 1 1 1.09280559898995e-16 1 Gldc +Mrps18b 3.11915524315591e-18 0.922377264946873 1 0.985 2.89145691040553e-15 1 Mrps18b +Mrpl15 2.30264233829135e-16 0.972099784208843 1 0.935 2.13454944759608e-13 1 Mrpl15 +Cbr2 8.18448617816477e-16 1.89511919465221 0.836 0.353 7.58701868715874e-13 1 Cbr2 +Obox6 1.16459567777946e-15 1.39344529354537 1 0.493 1.07958019330156e-12 1 Obox6 +Kng1 4.87786706844624e-15 1.69969555028587 0.925 0.428 4.52178277244966e-12 1 Kng1 +Ap4s1 4.38893882865998e-14 1.4030962183409 0.955 0.796 4.0685462941678e-11 1 Ap4s1 +Ppm1a 5.46198116048427e-14 1.05377847331112 1 0.99 5.06325653576892e-11 1 Ppm1a +Grb2 1.16712676944449e-13 1.08813878601354 1 0.95 1.08192651527504e-10 1 Grb2 +Lgals8 2.71992893350116e-12 1.06005256954461 1 0.92 2.52137412135557e-09 1 Lgals8 +Lctl 8.84118074688638e-12 1.49466351031029 0.97 0.846 8.19577455236367e-09 1 Lctl +Cand1 1.03564127623394e-11 0.739715256465815 1 1 9.60039463068864e-09 1 Cand1 +Wdr75 8.67327097764079e-11 0.850552684047768 1 0.975 8.04012219627302e-08 1 Wdr75 +Phldb3 1.39184779991039e-10 0.815038064101476 0.821 0.438 1.29024291051693e-07 1 Phldb3 +Atxn3 1.63475448330622e-10 0.87479476956743 1 0.94 1.51541740602487e-07 1 Atxn3 +Map2k2 2.002732323584e-10 0.723948311843295 1 0.955 1.85653286396237e-07 1 Map2k2 +Azin1 2.17732786063168e-10 0.672237856337222 1 0.98 2.01838292680557e-07 1 Azin1 +Stac2 2.2442574492249e-10 1.21105132168797 0.97 0.607 2.08042665543149e-07 1 Stac2 +Ovol2 4.36427022757736e-10 0.674300761897003 0.97 0.498 4.04567850096421e-07 1 Ovol2 +Tead4 1.05331028978453e-09 1.01726483975742 1 0.881 9.76418638630257e-07 1 Tead4 +Ccs 1.71739301526647e-09 1.17709398853197 0.97 0.831 1.59202332515202e-06 1 Ccs +Nin 5.48891568987971e-09 0.889936679587253 1 0.706 5.0882248445185e-06 1 Nin +Smarca4 2.70863773485621e-08 0.638133145992837 0.985 0.985 2.51090718021171e-05 1 Smarca4 +Slc25a20 3.99472396826257e-08 0.845590994412397 1 0.965 3.7031091185794e-05 1 Slc25a20 +1190007F08Rik 1.0003184979958e-07 0.869535629030856 0.896 0.687 9.2729524764211e-05 1 1190007F08Rik +Rpl36al1 1.49956646353042e-07 0.4310954898767 1 1 0.00013900981116927 1 Rpl36al +Sirt6 1.89914150279507e-07 0.618193903529396 1 0.975 0.000176050417309103 1 Sirt6 +Haus2 1.9462794092021e-07 0.827153932922399 0.985 0.91 0.000180420101233034 1 Haus2 +Lin28a 5.58858972877224e-07 0.783839963789619 0.985 0.731 0.000518062267857187 1 Lin28a +Rpl37a1 5.90899011890758e-07 0.482044967750386 1 1 0.000547763384022733 1 Rpl37a +Arrdc1 9.86700784057811e-07 0.711073533578284 0.881 0.687 0.000914671626821591 1 Arrdc1 +Trip13 1.06839483924259e-06 0.581215547508429 0.985 0.985 0.00099040201597788 1 Trip13 +Cnnm4 1.23939176532338e-06 0.618501508653815 0.985 0.856 0.00114891616645477 1 Cnnm4 +Nr1h3 1.32490727704543e-06 0.64977092326636 0.687 0.308 0.00122818904582111 1 Nr1h3 +Zfand2b 1.44487796912892e-06 0.783945342530844 0.955 0.806 0.00133940187738251 1 Zfand2b +Hprt 1.9771695574352e-06 0.641843173989667 1 1 0.00183283617974243 1 Hprt +Cbr1 2.080666391675e-06 0.695824528335629 0.985 0.92 0.00192877774508272 1 Cbr1 +Smap1 2.60599803541757e-06 0.670920002915592 1 0.93 0.00241576017883209 1 Smap1 +Trim54 3.56089316110149e-06 0.580088826909494 0.313 0.09 0.00330094796034109 1 Trim54 +Oxsr1 3.64730930662247e-06 0.806911377316181 0.985 0.896 0.00338105572723903 1 Oxsr1 +1190005F20Rik 4.99232920248389e-06 0.685672814249321 0.985 0.856 0.00462788917070256 1 1190005F20Rik +Prkrip1 5.99893248907293e-06 0.514240005237342 0.97 0.99 0.00556101041737061 1 Prkrip1 +Gtf2f2 1.40808077962277e-05 0.437162718926523 1 0.99 0.0130529088271031 1 Gtf2f2 +Hes1 1.55043756394457e-05 0.35192315833842 0.97 0.871 0.0143725562177662 1 Hes1 +Gemin5 1.95646562299594e-05 0.442174218669884 1 0.98 0.0181364363251724 1 Gemin5 +Tmem2081 2.14241690725616e-05 0.500673472600329 0.985 0.915 0.0198602047302646 1 Tmem208 +Myg1 2.84445872166292e-05 0.504473721332222 0.985 0.891 0.0263681323498153 1 Myg1 +Nek2 2.85869467954603e-05 0.28267666797816 1 0.94 0.0265000996793917 1 Nek2 +Brd2 2.86104267363888e-05 0.387442555193399 1 1 0.0265218655846324 1 Brd2 +Pitpnc1 4.32985895572162e-05 0.509398484389986 0.97 0.856 0.0401377925195394 1 Pitpnc1 +Unc45a 4.78568333344799e-05 0.494684374542451 0.925 0.731 0.0443632845010628 1 Unc45a +Arhgap1 6.17842158786466e-05 0.339065273903611 1 1 0.0572739681195054 1 Arhgap1 +Gatsl3 6.41587783549619e-05 0.613871855235264 1 0.94 0.0594751875350497 1 Gatsl3 +Polr2k 8.97657212260155e-05 0.332921899749521 1 0.99 0.0832128235765164 1 Polr2k +Gls 9.74962730724083e-05 0.7448456475451 1 0.96 0.0903790451381225 1 Gls +Gsdmc3 0.000122670702193285 0.289809744442694 0.552 0.313 0.113715740933176 1 Gsdmc3 +2700078E11Rik 0.000133299845253646 0.50934297769746 0.97 0.975 0.12356895655013 1 2700078E11Rik +Dnajc5g 0.000142081946287188 0.959223331044612 0.507 0.299 0.131709964208223 1 Dnajc5g +Pum2 0.00017864418057919 0.306318884284979 1 1 0.165603155396909 1 Pum2 +Rtn41 0.000220176700300593 0.383145822333726 1 1 0.204103801178649 1 Rtn4 +Abcc3 0.000225762861771427 0.536297193030252 0.746 0.483 0.209282172862113 1 Abcc3 +Smarcd3 0.00033745821895663 1.17980872789168 0.433 0.264 0.312823768972796 1 Smarcd3 +Jarid2 0.000341204661100151 0.323386394420202 1 1 0.31629672083984 1 Jarid2 +Gtpbp10 0.000493212064996593 0.358087678844319 0.94 0.866 0.457207584251841 1 Gtpbp10 +Wbscr22 0.000843447959223422 0.457443652954918 1 0.935 0.781876258200112 1 Wbscr22 +Irak2 0.000926379037174115 0.471729987082767 0.955 0.891 0.858753367460405 1 Irak2 +Zfp296 0.000926648396690121 0.468919586959273 0.985 0.925 0.859003063731742 1 Zfp296 +Ccdc9 0.000973910876381618 0.569371320537871 0.94 0.881 0.90281538240576 1 Ccdc9 +Camk2b 0.0010850881588712 0.377763682657377 0.597 0.413 1 1 Camk2b +Rassf7 0.00148419844200689 0.27676168753326 0.955 0.826 1 1 Rassf7 +Ipo11 0.00160952726587784 0.286184028428292 0.985 0.96 1 1 Ipo11 +Lyar 0.00191469481174217 0.308393205483807 1 0.995 1 1 Lyar +Egfl8 0.0020903942123629 0.526630836116279 0.313 0.154 1 1 Egfl8 +Sf3b4 0.00398502550224829 0.388067644888654 1 0.955 1 1 Sf3b4 +Rnaseh2b1 0.0040636868168902 0.395850931953736 0.985 0.881 1 1 Rnaseh2b +Clk2 0.00410047533283962 0.324865667998878 0.94 0.836 1 1 Clk2 +Tulp1 0.0042735737972395 0.627190830612499 0.418 0.249 1 1 Tulp1 +Ciao1 0.00428113709548694 0.370456060148884 0.955 0.955 1 1 Ciao1 +Eif3f 0.00538871083301758 0.273767031380469 1 0.99 1 1 Eif3f +Sf3b3 0.00796365566854649 0.315135535284671 1 0.995 1 1 Sf3b3 +Rpl361 0.00985699703684655 0.309831424904361 1 0.99 1 1 Rpl36 +Acot2 1.62353858683152e-29 2.7266845500104 1 0.507 1.50502026999282e-26 2 Acot2 +Tmsb10 3.02206767317863e-28 2.22392509606323 1 1 2.80145673303659e-25 2 Tmsb10 +Fabp3 1.39244941929966e-27 2.72699175689115 1 0.916 1.29080061169079e-24 2 Fabp3 +Enpep 4.46690414906521e-27 2.92670863133069 1 0.739 4.14082014618344e-24 2 Enpep +Tjp2 5.46327592939334e-27 2.45836196415643 1 0.892 5.06445678654762e-24 2 Tjp2 +Capg 7.22172135775103e-26 3.13679655037263 0.969 0.419 6.6945356986352e-23 2 Capg +Ptges 1.15835885784397e-22 1.62948908444797 1 0.936 1.07379866122136e-19 2 Ptges +Dapk1 1.85278765586486e-22 2.44672982424483 0.831 0.251 1.71753415698672e-19 2 Dapk1 +Dkkl1 1.17911698813629e-20 2.55632858100655 0.954 0.552 1.09304144800234e-17 2 Dkkl1 +Gpx4 8.31856912734218e-20 1.11281793654164 1 0.97 7.7113135810462e-17 2 Gpx4 +Scly 4.36658564644958e-18 1.80578569140075 0.877 0.404 4.04782489425876e-15 2 Scly +Il17re 1.01815869304518e-17 1.72205394102478 0.708 0.182 9.43833108452885e-15 2 Il17re +Vtcn1 1.93683892464856e-16 1.82727599994358 0.815 0.315 1.79544968314922e-13 2 Vtcn1 +D4Bwg0951e 2.42007193262114e-16 1.46056702698097 0.831 0.315 2.2434066815398e-13 2 D4Bwg0951e +Faah 6.7216429804354e-16 2.53867563610808 0.862 0.424 6.23096304286362e-13 2 Faah +Chmp2b 1.46817370650576e-14 1.98949875357205 0.908 0.532 1.36099702593084e-11 2 Chmp2b +Trp53bp2 5.37707971100586e-14 1.6647799908992 0.877 0.453 4.98455289210243e-11 2 Trp53bp2 +Pigz 6.24498554167431e-14 1.99622313089521 0.677 0.222 5.78910159713208e-11 2 Pigz +Slc20a1 6.46979346431305e-14 1.98869118023904 0.985 0.99 5.99749854141819e-11 2 Slc20a1 +Eno11 1.08931009706478e-13 0.45522985988319 0.969 0.596 1.00979045997905e-10 2 Eno1 +Gyltl1b 1.35524709716349e-13 1.77421980508475 0.908 0.631 1.25631405907055e-10 2 Gyltl1b +Cycs1 1.55505723320804e-13 0.999377186583543 1 0.995 1.44153805518385e-10 2 Cycs +Ptpra 1.92861792244247e-12 1.32786009011917 0.985 0.897 1.78782881410417e-09 2 Ptpra +Hint21 2.41626942776709e-12 1.06789237114775 0.923 0.488 2.23988175954009e-09 2 Hint2 +Coro7 3.5163514293472e-12 2.18220456517293 0.815 0.468 3.25965777500485e-09 2 Coro7 +Tmem1801 3.73037485779247e-12 1.56485007236385 0.862 0.414 3.45805749317362e-09 2 Tmem180 +2010300C02Rik 4.4006186207135e-12 2.01787656661514 0.754 0.394 4.07937346140142e-09 2 2010300C02Rik +Mkl1 8.49457286044839e-12 2.19959199640081 0.954 0.709 7.87446904163566e-09 2 Mkl1 +Ftl11 1.85816970732134e-11 0.787299952633541 1 1 1.72252331868688e-08 2 Ftl1 +Oplah 3.868914537176e-11 1.45321604449591 0.538 0.153 3.58648377596215e-08 2 Oplah +Cpped11 4.4213237260524e-11 1.53196291540956 0.877 0.502 4.09856709405057e-08 2 Cpped1 +Casp71 7.95740882439946e-11 1.65360729235441 0.785 0.424 7.3765179802183e-08 2 Casp7 +Xbp1 1.37423135469636e-10 1.51437698408037 0.969 0.67 1.27391246580353e-07 2 Xbp1 +Arhgap11 5.64341681761558e-10 0.790185184726235 1 1 5.23144738992964e-07 2 Arhgap1 +Rai141 1.19838811281811e-09 1.00184528083498 0.892 0.532 1.11090578058238e-06 2 Rai14 +Cox7a2l1 1.52250906115737e-09 0.677122222652421 1 0.98 1.41136589969288e-06 2 Cox7a2l +Cxxc5 6.60768689755903e-09 1.39290784859321 0.723 0.394 6.12532575403722e-06 2 Cxxc5 +Gsta2 7.54903465645573e-09 1.13492417222392 0.769 0.498 6.99795512653446e-06 2 Gsta2 +Gng101 9.69480767962571e-09 1.02400049457935 0.846 0.473 8.98708671901303e-06 2 Gng10 +Trpv6 1.30169804139126e-08 0.57056993157703 0.431 0.118 1.2066740843697e-05 2 Trpv6 +Exosc81 1.56766881950255e-08 0.623553710286937 1 1 1.45322899567886e-05 2 Exosc8 +Prelid11 3.65220983961452e-08 0.58507766020631 1 0.99 3.38559852132266e-05 2 Prelid1 +AW549877 3.95948261925056e-08 1.37975687982903 0.908 0.655 3.67044038804527e-05 2 AW549877 +Gpi11 6.6542462074963e-08 0.695370524461669 1 0.975 6.16848623434907e-05 2 Gpi1 +Chid1 9.67918053242398e-08 1.14584930091399 0.923 0.764 8.97260035355703e-05 2 Chid1 +Epb4.1 1.38701811868984e-07 0.892952001882638 0.985 0.911 0.000128576579602548 2 Epb4.1 +Sept21 1.39410386329695e-07 0.507604369330746 1 1 0.000129233428127627 2 Sept2 +Psen1 2.4655945232841e-07 1.01467124863334 0.938 0.926 0.000228560612308436 2 Psen1 +Pus101 3.06037080910438e-07 0.955577485466123 0.923 0.68 0.000283696374003976 2 Pus10 +Eif1a1 4.03192053477205e-07 0.469671811889738 1 0.995 0.000373759033573369 2 Eif1a +Myeov21 4.33418040846447e-07 0.668565366139197 0.985 0.985 0.000401778523864656 2 Myeov2 +Ip6k2 5.87799120148303e-07 0.709401405747517 0.815 0.562 0.000544889784377476 2 Ip6k2 +Fth11 6.69551039103819e-07 0.577836363179499 1 1 0.000620673813249241 2 Fth1 +Sra11 7.06412988138587e-07 0.672784671833007 0.985 0.921 0.00065484484000447 2 Sra1 +Ppl 1.26566925189732e-06 1.17704147049068 0.508 0.202 0.00117327539650881 2 Ppl +Fam82b 1.71169598208052e-06 0.419580457301326 0.492 0.197 0.00158674217538864 2 Fam82b +Fkbp21 1.97458719436916e-06 0.70615077131727 0.969 0.906 0.00183044232918021 2 Fkbp2 +Mrpl451 2.00385667353968e-06 0.566107233110735 0.969 0.99 0.00185757513637128 2 Mrpl45 +Rassf71 2.74648985052535e-06 0.923613983081832 0.923 0.837 0.002545996091437 2 Rassf7 +Ube2f 2.89493277828888e-06 0.78000923438236 0.969 0.931 0.00268360268547379 2 Ube2f +Fam122b 3.1473670749885e-06 1.23462858478077 0.892 0.665 0.00291760927851434 2 Fam122b +1700034O15Rik 3.23544394209349e-06 0.735071389184371 0.292 0.074 0.00299925653432067 2 1700034O15Rik +Mical1 4.46040709467345e-06 1.34817811535299 0.723 0.488 0.00413479737676229 2 Mical1 +B230120H23Rik 4.62296105462335e-06 0.957541743691926 0.738 0.498 0.00428548489763584 2 B230120H23Rik +Rbl1 4.63893601792003e-06 1.51403947053879 0.862 0.562 0.00430029368861187 2 Rbl1 +Ppp1r111 5.41394668071349e-06 0.636448869971692 0.985 0.966 0.00501872857302141 2 Ppp1r11 +Rab8a 5.73144700774355e-06 0.571144721699556 1 0.995 0.00531305137617827 2 Rab8a +Cyp4f39 5.74529568067207e-06 1.93283267372237 0.338 0.113 0.00532588909598301 2 Cyp4f39 +Ncstn 7.94134311392418e-06 1.2140672073807 0.954 0.931 0.00736162506660772 2 Ncstn +Hnrnpa01 8.90015651158464e-06 0.907347753972338 0.985 0.98 0.00825044508623896 2 Hnrnpa0 +Tcn2 9.20293781843428e-06 1.4844367153768 0.831 0.645 0.00853112335768858 2 Tcn2 +Herpud11 9.21626671522023e-06 1.07587657459569 0.538 0.281 0.00854347924500915 2 Herpud1 +Ap1m2 1.08176609061221e-05 0.856395828803297 0.969 0.956 0.0100279716599752 2 Ap1m2 +Ehd1 1.11879937217002e-05 0.709145097902885 1 0.941 0.0103712701800161 2 Ehd1 +Tns11 1.17399966016812e-05 0.534193539647709 0.862 0.522 0.0108829768497584 2 Tns1 +Fnbp1l 1.84978029238725e-05 0.438601494003316 0.954 0.808 0.0171474633104298 2 Fnbp1l +Gga1 3.72875804953036e-05 1.03592536201296 0.938 0.842 0.0345655871191464 2 Gga1 +Abhd111 4.10955520917889e-05 0.668138917939135 0.954 0.985 0.0380955767890883 2 Abhd11 +Ankrd33b 6.90639991906004e-05 0.791889041644608 0.446 0.217 0.0640223272496866 2 Ankrd33b +Reep31 9.4412978119217e-05 0.729799939615274 0.923 0.837 0.0875208307165141 2 Reep3 +Tbrg11 0.000103820148803723 0.439549570629096 1 0.995 0.0962412779410508 2 Tbrg1 +Lancl1 0.000103843943128829 1.10043428084716 0.938 0.857 0.0962633352804241 2 Lancl1 +Ube2r2 0.000109801804354686 0.538615363891787 0.969 0.901 0.101786272636794 2 Ube2r2 +Ube4a 0.00013246680402732 0.80231311462887 0.985 0.956 0.122796727333326 2 Ube4a +Zfp7041 0.000141057410378776 0.554369380378906 0.969 0.842 0.130760219421125 2 Zfp704 +Synj2bp1 0.000159031917407965 0.585551941509249 0.923 0.828 0.147422587437183 2 Synj2bp +Acp51 0.00017849899391098 0.673371406737795 0.938 0.808 0.165468567355478 2 Acp5 +Slc18a1 0.000179564491720651 1.94884846509656 0.308 0.128 0.166456283825043 2 Slc18a1 +Stx4a 0.000219317843397067 0.935664343526722 0.877 0.788 0.203307640829081 2 Stx4a +Mllt4 0.000239020863454647 0.710509512220825 0.985 0.97 0.221572340422458 2 Mllt4 +Jarid21 0.000246028862359803 0.41037939191042 1 1 0.228068755407537 2 Jarid2 +Tapbpl 0.000253703579432621 0.300077204995076 0.938 0.783 0.235183218134039 2 Tapbpl +Fam173a 0.000296114375973877 0.779293669944395 0.8 0.69 0.274498026527784 2 Fam173a +Fam118b 0.000308247544060562 0.890214303677844 0.938 0.921 0.285745473344141 2 Fam118b +Ehmt2 0.00030997616175819 0.804593481454567 0.954 0.877 0.287347901949842 2 Ehmt2 +App 0.000317562895932702 0.908960272607608 0.523 0.32 0.294380804529615 2 App +Mea11 0.000318011880769364 0.342503452163259 0.985 0.99 0.294797013473201 2 Mea1 +Nucks11 0.000329446924394209 0.341111576898772 1 1 0.305397298913432 2 Nucks1 +Sap181 0.000438784421802869 0.507468892193082 1 0.99 0.40675315901126 2 Sap18 +Ccdc50 0.00044045114017215 0.26306333404998 0.908 0.719 0.408298206939583 2 Ccdc50 +Rpl362 0.000510596669621397 0.40531985559223 1 0.99 0.473323112739035 2 Rpl36 +Slamf9 0.000570582927195888 1.82906110129345 0.308 0.138 0.528930373510588 2 Slamf9 +Zdhhc61 0.000577283782296124 0.710163044924531 0.923 0.916 0.535142066188507 2 Zdhhc6 +Laptm4a1 0.000721272110097679 0.420671113163927 1 0.985 0.668619246060548 2 Laptm4a +Mrpl511 0.000760868454372259 0.345850805664343 0.985 1 0.705325057203084 2 Mrpl51 +Cyp4f131 0.000864131391558196 0.362168158683275 0.323 0.148 0.801049799974447 2 Cyp4f13 +Mtdh1 0.000955824694399856 0.533092823109913 0.985 0.995 0.886049491708666 2 Mtdh +St3gal3 0.00126575405660349 0.529427517738675 0.415 0.222 1 2 St3gal3 +Comt1 0.0015540585563039 0.590357542823012 1 1 1 2 Comt +Npr11 0.00166645968355906 0.597683431409277 0.877 0.803 1 2 Npr1 +Slc35c1 0.00212375092449243 0.358368850206992 0.831 0.591 1 2 Slc35c1 +Cdk18 0.00228713090797904 0.546450428708579 0.769 0.532 1 2 Cdk18 +Cnnm41 0.00241226408290813 0.861855143991789 0.938 0.872 1 2 Cnnm4 +Mid1ip1 0.00261674048336717 0.393483261929315 0.492 0.276 1 2 Mid1ip1 +0610010K14Rik1 0.00270937087096939 0.302639639454223 0.985 0.98 1 2 0610010K14Rik +1190007F08Rik1 0.00298379888138995 0.420010342700349 0.892 0.69 1 2 1190007F08Rik +Trip11 0.00383410846701351 0.873694732823184 0.892 0.754 1 2 Trip11 +Zdhhc3 0.00417409303565624 0.48513242124485 0.985 0.98 1 2 Zdhhc3 +Hist1h1d 0.00468675162600295 0.403987110231785 0.769 0.704 1 2 Hist1h1d +Msrb21 0.00488129915739156 0.506516677710613 0.615 0.429 1 2 Msrb2 +Calu1 0.00490491939469693 0.574241101221317 1 0.975 1 2 Calu +Osgep 0.00572801134361098 0.612827341368115 0.877 0.867 1 2 Osgep +Haus81 0.00616393064050853 0.395131825000314 0.954 0.946 1 2 Haus8 +Atp6v1c11 0.00646709393955921 0.334593779222677 1 0.995 1 2 Atp6v1c1 +Nde1 0.00665389076361832 0.929107214909593 0.8 0.709 1 2 Nde1 +Shc1 0.00697545537058933 0.480112773425593 0.985 0.901 1 2 Shc1 +Lct 0.0073133650332465 0.974586289018096 0.338 0.187 1 2 Lct +Hspa5 0.0084174351925224 0.345792711303401 1 0.995 1 2 Hspa5 +Mrpl171 0.00846313073174018 0.307088282758327 1 0.99 1 2 Mrpl17 +9130024F11Rik 0.00893308535166574 0.878439451763501 0.538 0.389 1 2 9130024F11Rik +Ctnnb11 0.00942506764753194 0.306914797084541 1 0.99 1 2 Ctnnb1 +Gm13718 1.55630538391193e-19 2.92808805098703 1 0.553 1.44269509088636e-16 3 Gm13718 +Tor1b 4.62284548705192e-19 2.2436505047392 1 0.904 4.28537776649713e-16 3 Tor1b +Nr1h31 5.3276131958828e-17 2.254455958601 0.9 0.316 4.93869743258336e-14 3 Nr1h3 +Obox61 9.18123901672887e-17 2.00047679908422 1 0.553 8.51100856850766e-14 3 Obox6 +Nek21 7.13590385447324e-15 1.83454980773476 1 0.947 6.6149828730967e-12 3 Nek2 +Nin1 1.17214942833535e-14 1.62662634272488 1 0.741 1.08658252006687e-11 3 Nin +Zfyve27 2.45672576751913e-14 1.73965272001361 1 0.754 2.27738478649024e-11 3 Zfyve27 +Ranbp10 5.42706519275376e-14 1.59852410703371 1 0.895 5.03088943368273e-11 3 Ranbp10 +Tekt2 6.49940283992347e-14 2.82997989947872 0.875 0.404 6.02494643260906e-11 3 Tekt2 +Gm4850 2.04668522398056e-13 2.15052012665154 0.65 0.14 1.89727720262998e-10 3 Gm4850 +Arrdc11 3.25174842897428e-13 1.90374874419383 1 0.689 3.01437079365916e-10 3 Arrdc1 +Rbm42 3.45762896297788e-13 1.54683075865269 1 0.978 3.20522204868049e-10 3 Rbm42 +Ovol21 6.25030711844577e-13 1.73324516625763 1 0.548 5.79403469879923e-10 3 Ovol2 +Cand11 7.19332048296455e-13 0.901879472185876 1 1 6.66820808770814e-10 3 Cand1 +4632434I11Rik 8.67280047856193e-13 1.58246196955888 1 0.925 8.03968604362691e-10 3 4632434I11Rik +Tnfrsf19 1.66301223020286e-12 0.82667159286793 0.525 0.088 1.54161233739805e-09 3 Tnfrsf19 +Gpatch3 2.20502413126683e-12 1.23493164448555 0.875 0.333 2.04405736968435e-09 3 Gpatch3 +Brd21 2.50180512587374e-12 1.15192781085977 1 1 2.31917335168495e-09 3 Brd2 +Ythdf2 6.39767114821792e-12 1.01541463864112 1 1 5.93064115439802e-09 3 Ythdf2 +Mta2 9.24398470133752e-12 1.46768725008642 1 0.943 8.56917381813988e-09 3 Mta2 +Fez1 1.33738640996328e-11 1.5432232344154 0.6 0.145 1.23975720203596e-08 3 Fez1 +Lyar1 1.58371717351037e-11 0.914139077595804 1 0.996 1.46810581984411e-08 3 Lyar +Siah1a 1.7008389049071e-11 1.69136082592614 1 0.785 1.57667766484888e-08 3 Siah1a +Abt1 1.9876605632386e-11 1.25639417278805 1 0.965 1.84256134212218e-08 3 Abt1 +Ddx52 2.73055597767851e-11 0.874610577716506 1 0.978 2.53122539130798e-08 3 Ddx52 +Mios 1.05404215313626e-10 1.73142666984655 0.975 0.789 9.77097075957316e-08 3 Mios +Hspa1a 1.45342882478114e-10 1.27343701330999 0.725 0.25 1.34732852057211e-07 3 Hspa1a +Synpr 1.67991303232505e-10 0.568121109730388 0.5 0.101 1.55727938096532e-07 3 Synpr +Dnajc5g1 1.91087296975842e-10 1.03500075456796 0.825 0.268 1.77137924296605e-07 3 Dnajc5g +Scfd2 4.1592156131485e-10 1.62178211791607 0.925 0.618 3.85559287338866e-07 3 Scfd2 +Zkscan14 5.50373341437281e-10 1.59683417673034 0.9 0.557 5.10196087512359e-07 3 Zkscan14 +Pum21 6.21463078996004e-10 0.852229791150654 1 1 5.76096274229296e-07 3 Pum2 +Fem1c 1.02180423461807e-09 1.58189626175518 0.95 0.825 9.47212525490955e-07 3 Fem1c +Cbl 1.19052966699622e-09 1.23369620729729 0.975 0.908 1.1036210013055e-06 3 Cbl +Tead41 1.70805521715344e-09 1.1433535820356 1 0.895 1.58336718630124e-06 3 Tead4 +Dnaja2 1.95718080517284e-09 0.774803462928394 1 0.996 1.81430660639522e-06 3 Dnaja2 +Ammecr1l 3.00770441943089e-09 1.32549221679247 1 0.93 2.78814199681244e-06 3 Ammecr1l +Gemin51 3.06000957980181e-09 1.06411774120896 1 0.982 2.83662888047628e-06 3 Gemin5 +Siah1b 3.13919366653555e-09 0.924220044885665 0.975 0.75 2.91003252887846e-06 3 Siah1b +Tssc4 3.32812903331153e-09 1.24580601411484 1 0.614 3.08517561387979e-06 3 Tssc4 +A630001G21Rik 4.66510774226657e-09 0.903575801457337 0.65 0.232 4.32455487708111e-06 3 A630001G21Rik +Med9 5.28134110511831e-09 1.25045611121759 0.975 0.803 4.89580320444467e-06 3 Med9 +Tmem87b 6.0941983739495e-09 1.10611395715927 1 0.825 5.64932189265118e-06 3 Tmem87b +Prrt4 6.93953016291568e-09 0.364925734697245 0.45 0.096 6.43294446102284e-06 3 Prrt4 +Ap4s11 1.49440195064723e-08 1.00326881440109 1 0.807 1.38531060824998e-05 3 Ap4s1 +Gldc1 1.89946441034918e-08 0.997220048328316 1 1 1.76080350839369e-05 3 Gldc +Fah 2.10746829251835e-08 0.651575892015608 0.4 0.088 1.95362310716451e-05 3 Fah +Wdr751 2.18588281896775e-08 0.991476658999314 1 0.978 2.0263133731831e-05 3 Wdr75 +Gtf2f21 2.85432712663989e-08 0.78330970047011 1 0.991 2.64596124639517e-05 3 Gtf2f2 +Abca13 3.50941538562996e-08 1.84050884015487 0.85 0.588 3.25322806247897e-05 3 Abca13 +Cops6 3.53679600540343e-08 0.643066174994073 1 1 3.27860989700898e-05 3 Cops6 +Nags 3.93151116293766e-08 0.960757943879068 0.3 0.044 3.64451084804322e-05 3 Nags +Kcng3 4.85464410756298e-08 0.550350133025919 0.325 0.057 4.50025508771088e-05 3 Kcng3 +Arid5a 5.339683390536e-08 1.4073852730954 0.725 0.325 4.94988650302687e-05 3 Arid5a +Bcl2l13 5.67693899055944e-08 0.886821407392687 1 0.952 5.2625224442486e-05 3 Bcl2l13 +Bcl2l14 1.24458791735209e-07 1.00682015784549 1 0.811 0.000115373299938539 3 Bcl2l14 +Stac21 1.33476583843622e-07 1.08985882317904 0.975 0.649 0.000123732793223037 3 Stac2 +Gm16515 1.44722738855689e-07 0.82844253225298 1 0.851 0.000134157978919224 3 Gm16515 +Larp41 1.45464990205996e-07 0.828721571407412 1 0.987 0.000134846045920958 3 Larp4 +Mosc2 1.70054414631204e-07 0.952390504584128 0.975 0.737 0.000157640442363126 3 Mosc2 +6720489N17Rik 2.54505932746399e-07 1.24609329910962 1 0.961 0.000235926999655912 3 6720489N17Rik +Zbtb37 2.73143742212281e-07 1.22137996609432 0.8 0.421 0.000253204249030784 3 Zbtb37 +Kctd20 2.9609942379847e-07 1.06049260032024 1 0.882 0.000274484165861181 3 Kctd20 +Usp37 3.9268236458702e-07 0.80923574390676 1 0.969 0.000364016551972168 3 Usp37 +Dcdc2c 4.77927598698933e-07 1.68661966286335 0.775 0.675 0.000443038883993911 3 Dcdc2c +Tinf2 7.88802857665619e-07 1.01666907179631 1 0.877 0.000731220249056029 3 Tinf2 +Ankrd52 1.07147810790233e-06 0.463270249082338 0.95 0.596 0.000993260206025459 3 Ankrd52 +Tysnd1 1.56491042185116e-06 1.07421382536886 0.9 0.667 0.00145067196105602 3 Tysnd1 +Zfp2961 1.59706270778083e-06 0.885685974211324 1 0.93 0.00148047713011283 3 Zfp296 +Gm7609 1.62825045805861e-06 0.517996199572675 0.65 0.386 0.00150938817462034 3 Gm7609 +Gal3st2 1.98629153312941e-06 0.948006024227831 0.55 0.202 0.00184129225121096 3 Gal3st2 +Slc16a5 2.39145864530177e-06 0.919490270035023 0.75 0.434 0.00221688216419474 3 Slc16a5 +Gtf3c3 2.60630856479299e-06 0.741241560980853 1 0.912 0.0024160480395631 3 Gtf3c3 +St3gal2 2.67554111945925e-06 0.653262933756673 0.775 0.395 0.00248022661773872 3 St3gal2 +Cep63 2.89988951768142e-06 0.902373644629461 0.95 0.851 0.00268819758289068 3 Cep63 +Rspry1 3.13367256828903e-06 1.27870948575483 0.875 0.715 0.00290491447080393 3 Rspry1 +Pole4 3.52061296249244e-06 0.759390975576141 1 0.908 0.00326360821623049 3 Pole4 +Tulp11 4.80063697592504e-06 0.787254789073524 0.575 0.241 0.00445019047668251 3 Tulp1 +Cry2 5.58121198396382e-06 1.15911909414641 0.85 0.518 0.00517378350913446 3 Cry2 +2810021B07Rik 7.39910145302197e-06 0.645102763935281 0.925 0.746 0.00685896704695137 3 2810021B07Rik +Rbbp6 8.54847551796692e-06 1.41393491969306 1 0.978 0.00792443680515533 3 Rbbp6 +Ikbkg 8.81372471604703e-06 0.661638825835279 1 0.961 0.00817032281177559 3 Ikbkg +Slc25a23 9.24702655028913e-06 0.819061653097851 0.875 0.482 0.00857199361211803 3 Slc25a23 +4930562C15Rik 9.77487361708448e-06 0.376144250929733 0.325 0.083 0.00906130784303731 3 4930562C15Rik +Polh 9.97221469227103e-06 0.538870604528395 0.7 0.338 0.00924424301973524 3 Polh +Gamt 1.01155957163578e-05 0.550427363896453 0.625 0.281 0.00937715722906367 3 Gamt +Clip2 1.04534383380878e-05 0.353979209516515 0.85 0.474 0.00969033733940738 3 Clip2 +Eif3f1 1.09316691215982e-05 0.437390979673951 1 0.991 0.0101336572757215 3 Eif3f +Zfp281 1.12080223701707e-05 0.703935181393964 1 0.904 0.0103898367371482 3 Zfp281 +Dtnb 1.22143889677681e-05 0.753805416175267 0.95 0.689 0.011322738573121 3 Dtnb +Timm17a1 1.27298530849986e-05 0.517342299672222 1 0.996 0.0118005738097937 3 Timm17a +Zfp346 1.56114947778694e-05 0.934846256683645 0.85 0.544 0.0144718556590849 3 Zfp346 +Kin 1.78878300032585e-05 0.667941909768243 1 0.943 0.0165820184130206 3 Kin +Smg5 2.22672961283151e-05 0.475753204558858 1 0.982 0.0206417835109481 3 Smg5 +Ppm1a1 2.43284463035723e-05 0.697290544655893 1 0.991 0.0225524697234115 3 Ppm1a +Serpini1 2.51660066488827e-05 0.672156042772623 0.525 0.202 0.0233288881635143 3 Serpini1 +Ypel5 3.32199098909373e-05 0.357268154388622 1 0.974 0.0307948564688989 3 Ypel5 +Alox12 3.40388861435749e-05 0.74670540735589 0.9 0.684 0.0315540474550939 3 Alox12 +Lctl1 4.03717505670797e-05 0.553522345092418 0.975 0.86 0.0374246127756829 3 Lctl +Azin11 4.06543217479778e-05 0.517482918084604 1 0.982 0.0376865562603754 3 Azin1 +Mgea5 4.55490069006865e-05 0.923806401696948 1 0.947 0.0422239293969364 3 Mgea5 +Lin54 4.68325312988345e-05 0.757413194081508 0.975 0.803 0.0434137565140195 3 Lin54 +Ipo111 4.87005029728353e-05 0.675573587929389 1 0.961 0.0451453662558183 3 Ipo11 +Cbr21 4.87267265724762e-05 0.880136909888852 0.8 0.417 0.0451696755326854 3 Cbr2 +Grb21 5.05738573440151e-05 0.790971997746518 1 0.956 0.046881965757902 3 Grb2 +Marveld1 5.47627579079715e-05 0.702535205475529 0.3 0.079 0.0507650765806896 3 Marveld1 +Prkrip11 5.93795487212108e-05 0.587235939441776 1 0.982 0.0550448416645624 3 Prkrip1 +Rnf135 5.93906926028215e-05 0.550001369144125 0.7 0.342 0.0550551720428155 3 Rnf135 +Apitd1 8.93164415615645e-05 1.02198724673295 0.975 0.908 0.0827963413275703 3 Apitd1 +Usp54 9.11694743054355e-05 0.55155848406849 0.975 0.768 0.0845141026811387 3 Usp54 +Dnd1 9.77488202357468e-05 0.314063103615636 0.8 0.439 0.0906131563585373 3 Dnd1 +Atxn31 9.86903587376627e-05 0.550416936132436 1 0.947 0.0914859625498133 3 Atxn3 +Nanos3 0.000118319467321025 0.288249210888947 0.4 0.14 0.10968214620659 3 Nanos3 +Pus1 0.000120694448486087 0.902281921087955 0.975 0.886 0.111883753746602 3 Pus1 +Ankrd57 0.000140616960404832 0.695430800639699 0.7 0.399 0.130351922295279 3 Ankrd57 +Kif9 0.000151686897984932 0.637936067073427 0.725 0.399 0.140613754432032 3 Kif9 +Nup43 0.000164848761816505 0.484307186299848 1 0.978 0.1528148022039 3 Nup43 +Slc39a9 0.000175979160452103 0.462066073543568 0.975 0.833 0.163132681739099 3 Slc39a9 +Smarcd31 0.000177648609119219 0.381059570775661 0.575 0.259 0.164680260653516 3 Smarcd3 +Bet1l 0.00019363662382668 0.731455876328385 0.975 0.82 0.179501150287332 3 Bet1l +Trpc6 0.000216967398764072 1.17172270612097 0.45 0.211 0.201128778654294 3 Trpc6 +Nfatc3 0.000220256841601569 0.67514627443187 1 0.982 0.204178092164654 3 Nfatc3 +Rsph1 0.000252412214170679 0.424861213515294 0.975 0.768 0.23398612253622 3 Rsph1 +Rasd2 0.000258522552751752 0.677513792756379 0.425 0.18 0.239650406400874 3 Rasd2 +Rtkn2 0.000259711802862102 0.692854334900885 0.6 0.329 0.240752841253168 3 Rtkn2 +Map2k21 0.000287763436969231 0.975061052454877 1 0.961 0.266756706070477 3 Map2k2 +Dda1 0.000301653389426777 0.733523682747304 0.975 0.904 0.279632691998622 3 Dda1 +Rgp1 0.000370166780186171 0.732579023830497 0.875 0.667 0.343144605232581 3 Rgp1 +Fadd 0.000382843399778255 0.610352661606133 0.925 0.785 0.354895831594442 3 Fadd +Ryr3 0.000434619803168513 0.426525286332399 0.475 0.211 0.402892557537212 3 Ryr3 +Kitl 0.000438480674973238 0.827896888960082 0.375 0.149 0.406471585700191 3 Kitl +Cdca4 0.000448923643471584 0.509023670014068 1 0.912 0.416152217498159 3 Cdca4 +Smurf2 0.000455542250118025 0.631367611251586 1 0.895 0.422287665859409 3 Smurf2 +Cd3eap 0.000464827257427677 0.809482843732468 0.975 0.939 0.430894867635456 3 Cd3eap +Donson 0.000482956890764624 0.54424829487314 0.925 0.711 0.447701037738807 3 Donson +Rnf41 0.000484087610977689 0.481893546993268 1 0.921 0.448749215376318 3 Rnf41 +Ctps2 0.000577147182858968 0.469895990756006 0.85 0.618 0.535015438510263 3 Ctps2 +Mgat4a 0.000595813809027286 0.444112072105756 0.975 0.794 0.552319400968294 3 Mgat4a +Zfp830 0.00062654091656072 0.566904277885787 0.975 0.886 0.580803429651787 3 Zfp830 +Trip131 0.000640889087350901 0.690984212378081 1 0.982 0.594104183974285 3 Trip13 +Imp4 0.000678281544321928 0.371995591086753 1 0.982 0.628766991586427 3 Imp4 +Gatad2a 0.000842348256187025 0.290880107938365 1 0.996 0.780856833485372 3 Gatad2a +Phldb31 0.00104932718436517 0.258385700777237 0.775 0.491 0.972726299906515 3 Phldb3 +Kng11 0.00109422336478314 0.545089544022897 0.8 0.509 1 3 Kng1 +Lrp12 0.00110394757727409 0.394821249352309 0.45 0.211 1 3 Lrp12 +Hspa51 0.0011273153287225 0.447496230944877 1 0.996 1 3 Hspa5 +Oxsr11 0.00124792687066747 0.529769571895526 0.975 0.908 1 3 Oxsr1 +Sar1a 0.00128610674469166 0.42341679297363 1 0.991 1 3 Sar1a +Lnpep 0.00129957284754789 0.343384292663078 0.85 0.579 1 3 Lnpep +Rnf25 0.00136466454250063 0.530419895031632 0.95 0.781 1 3 Rnf25 +Nmb 0.00144538437621593 0.689128741152352 0.85 0.737 1 3 Nmb +Gla 0.00160417091121791 0.335257471966212 1 0.939 1 3 Gla +Tmem189 0.00185656942599541 0.320984728364218 0.9 0.61 1 3 Tmem189 +Nop161 0.00214957840407835 0.499316771229331 1 0.956 1 3 Nop16 +Lmod3 0.00224675994090999 0.786084968080782 0.35 0.149 1 3 Lmod3 +Nlrp3 0.00242962160054685 0.304634825815689 0.425 0.224 1 3 Nlrp3 +Eif2ak3 0.0024918981730553 0.448293072349913 0.95 0.842 1 3 Eif2ak3 +2400003C14Rik 0.00252763699254032 0.317480947316878 1 0.991 1 3 2400003C14Rik +Kcnj13 0.00257259541382094 0.334677804278403 0.375 0.171 1 3 Kcnj13 +Fgfr1op 0.00308491557346444 0.506071436938047 1 0.895 1 3 Fgfr1op +Zmym3 0.0033216354587185 0.412076405893259 0.95 0.811 1 3 Zmym3 +Sirt61 0.00408088405471229 0.525572574329067 1 0.978 1 3 Sirt6 +Irak21 0.00448285863365471 0.577804642764755 0.95 0.899 1 3 Irak2 +Vmn1r32 0.00511738028239428 0.387122034480188 0.25 0.101 1 3 Vmn1r32 +Abcc31 0.00544532843658574 0.587606389469099 0.75 0.513 1 3 Abcc3 +Ccdc91 0.0057109864272939 0.539603426200726 0.975 0.882 1 3 Ccdc9 +2900060B14Rik 0.00587816461322828 0.364878988587328 0.725 0.645 1 3 2900060B14Rik +Prr24 0.00601994942633764 0.437029736135273 0.4 0.211 1 3 Prr24 +Mtf1 0.00649515834703391 0.373933103385015 1 0.934 1 3 Mtf1 +Smarca41 0.00667582194536819 0.317989195368421 1 0.982 1 3 Smarca4 +Trim40 0.00675738941838751 0.650756590457196 0.3 0.136 1 3 Trim40 +Hgs 0.00681028334675727 0.547553600771014 1 0.969 1 3 Hgs +Mapk14 0.00757557296917801 0.495354797527539 0.925 0.908 1 3 Mapk14 +Upk1a 0.00850416694353715 0.258271217639701 0.275 0.114 1 3 Upk1a +Nrg1 0.00923011271724026 0.427030692583274 0.275 0.118 1 3 Nrg1 +Zfp46 0.00999509585279969 0.456427763509172 0.525 0.329 1 3 Zfp46 +Calb1 7.28647433729453e-42 1.45954347817052 0.84 0.016 6.75456171067202e-39 4 Calb1 +Tekt4 1.79341146505131e-38 1.19411595781962 0.8 0.021 1.66249242810257e-35 4 Tekt4 +Gm4788 6.10457512617732e-37 0.289372363830689 0.96 0.053 5.65894114196637e-34 4 Gm4788 +Gm14446 9.83486754025169e-37 1.10612269093507 0.92 0.053 9.11692220981331e-34 4 Gm14446 +Trp63 1.34502369760313e-35 3.75677184609127 1 0.082 1.2468369676781e-32 4 Trp63 +Ctsm 1.37373256961556e-35 0.624944487660198 0.8 0.029 1.27345009203362e-32 4 Ctsm +Gstt1 1.98151913030037e-34 2.06705584204653 0.92 0.062 1.83686823378844e-31 4 Gstt1 +Tox 5.39398346941271e-34 2.12071714048673 0.96 0.078 5.00022267614559e-31 4 Tox +Nanos2 5.49283398452429e-34 4.04192499690346 1 0.095 5.09185710365402e-31 4 Nanos2 +Prelp 2.53835154072561e-33 2.62174839925537 0.96 0.078 2.35305187825264e-30 4 Prelp +Sh3rf2 3.57723995960802e-33 1.0899391995644 0.88 0.049 3.31610144255664e-30 4 Sh3rf2 +Emilin2 4.23851587721419e-33 2.45843497343143 0.96 0.078 3.92910421817756e-30 4 Emilin2 +Stk32b 1.53392517533364e-31 2.4205000656676 0.92 0.082 1.42194863753429e-28 4 Stk32b +Ppp1r3d 1.79261030218208e-31 2.43909233907224 0.96 0.091 1.66174975012279e-28 4 Ppp1r3d +Palm2 1.12426469838009e-30 2.27146604034126 0.96 0.095 1.04219337539834e-27 4 Palm2 +Postn 1.72476598681431e-30 2.95539793427314 0.92 0.086 1.59885806977686e-27 4 Postn +Dnajb4 3.47329353730143e-29 5.71514550118603 1 0.136 3.21974310907843e-26 4 Dnajb4 +7420461P10Rik 5.12122030704543e-29 3.5088182124285 0.96 0.123 4.74737122463111e-26 4 7420461P10Rik +Slc4a10 7.44635002670757e-29 1.27631043307641 0.8 0.058 6.90276647475792e-26 4 Slc4a10 +Zfp735 7.57629903274414e-29 4.28111410619815 0.96 0.123 7.02322920335382e-26 4 Zfp735 +Gbp7 1.14781355868572e-28 2.42296497879866 1 0.128 1.06402316890166e-25 4 Gbp7 +Clip4 1.49221307271991e-28 1.42269149725122 0.92 0.099 1.38328151841136e-25 4 Clip4 +St8sia6 2.05436346012464e-28 1.3029691191917 0.72 0.037 1.90439492753555e-25 4 St8sia6 +St6gal1 2.89302932572725e-28 4.80291341516131 1 0.156 2.68183818494916e-25 4 St6gal1 +Syt7 3.09282493012009e-28 2.24029250619211 0.92 0.099 2.86704871022133e-25 4 Syt7 +Cntn4 4.83347647917491e-28 3.10497248917219 0.96 0.128 4.48063269619515e-25 4 Cntn4 +Ctnna3 4.92707395082766e-28 3.39397095813409 1 0.144 4.56739755241725e-25 4 Ctnna3 +Nlgn3 5.25745326168359e-28 1.66716469124238 0.84 0.074 4.87365917358069e-25 4 Nlgn3 +Map3k13 5.49459151249972e-28 1.10392474699485 0.88 0.078 5.09348633208724e-25 4 Map3k13 +4930555I21Rik 1.14573801368869e-27 0.951739844147589 0.72 0.041 1.06209913868942e-24 4 4930555I21Rik +Kitl1 1.45490984971873e-27 1.62088904807932 0.96 0.103 1.34870143068926e-24 4 Kitl +AA619741 1.35394401159613e-26 5.37344873396987 1 0.181 1.25510609874961e-23 4 AA619741 +Wbscr17 2.12766491872281e-26 1.25489622698818 0.84 0.078 1.97234537965604e-23 4 Wbscr17 +Pde1c 3.57295725986617e-26 1.86155376062952 0.92 0.115 3.31213137989594e-23 4 Pde1c +Nlrp2 4.03551648464834e-26 3.87883801804513 1 0.169 3.74092378126901e-23 4 Nlrp2 +Pparg 1.50672978059141e-25 1.82928193004598 0.8 0.074 1.39673850660823e-22 4 Pparg +4930503L19Rik 1.72631465635943e-25 3.09157524056451 1 0.156 1.60029368644519e-22 4 4930503L19Rik +Fbxl21 1.80349338256092e-25 1.57379295498457 0.92 0.099 1.67183836563397e-22 4 Fbxl21 +Rgs12 1.93831869055277e-25 2.01250447557147 0.96 0.144 1.79682142614242e-22 4 Rgs12 +Casp8 1.95919400228315e-25 4.73350218345289 0.84 0.095 1.81617284011648e-22 4 Casp8 +Rasgef1b 2.11363002941664e-25 1.56148954106681 0.92 0.119 1.95933503726923e-22 4 Rasgef1b +Fam107a 2.75945482625141e-25 1.7432003603996 0.96 0.144 2.55801462393506e-22 4 Fam107a +A1bg 3.66818608849822e-25 1.75093545418898 0.8 0.082 3.40040850403785e-22 4 A1bg +Agbl2 7.33120966605028e-25 3.91176442309137 0.96 0.177 6.79603136042861e-22 4 Agbl2 +Add2 7.71538999268531e-25 1.7491113223912 0.88 0.103 7.15216652321928e-22 4 Add2 +Tnik 1.89195523311494e-24 2.96776212755676 1 0.181 1.75384250109755e-21 4 Tnik +Gm13103 1.98202827765328e-24 1.48618708207435 1 0.222 1.83734021338459e-21 4 Gm13103 +Siglec5 2.2391211140376e-24 0.405399213309922 0.72 0.053 2.07566527271286e-21 4 Siglec5 +Synj2 2.33009316301787e-24 1.68164354097269 0.96 0.169 2.15999636211757e-21 4 Synj2 +Cyp19a1 2.35801545558747e-24 1.327668131859 0.56 0.021 2.18588032732959e-21 4 Cyp19a1 +Flrt3 2.48336149544909e-24 3.84695080774018 1 0.206 2.3020761062813e-21 4 Flrt3 +Aass 1.35916865073072e-23 3.40078224674518 0.96 0.169 1.25994933922737e-20 4 Aass +D630045J12Rik 1.62506771843295e-23 1.84527551695428 0.92 0.148 1.50643777498734e-20 4 D630045J12Rik +Jazf1 1.87738199888022e-23 4.34215562795256 1 0.226 1.74033311296197e-20 4 Jazf1 +Ptprh 2.32885897414176e-23 1.07490162368816 0.92 0.115 2.15885226902941e-20 4 Ptprh +Fgf8 4.85917909242449e-23 0.525503954122529 0.72 0.062 4.5044590186775e-20 4 Fgf8 +Nlrp9b 5.06014614181235e-23 5.86506970992502 1 0.255 4.69075547346005e-20 4 Nlrp9b +Dnaja4 5.37627291326716e-23 2.90342957836727 0.96 0.169 4.98380499059865e-20 4 Dnaja4 +Dkk3 9.98611410003035e-23 1.01811035604314 0.64 0.041 9.25712777072813e-20 4 Dkk3 +Tspyl4 1.58282432303781e-22 3.41885162653521 0.96 0.193 1.46727814745605e-19 4 Tspyl4 +4931408C20Rik 4.03471252761375e-22 2.96899781057889 0.84 0.119 3.74017851309795e-19 4 4931408C20Rik +Cldn15 6.93072480095987e-22 1.61506025710929 0.76 0.082 6.4247818904898e-19 4 Cldn15 +Klhdc1 2.3666867357006e-21 1.54006665271039 0.92 0.144 2.19391860399446e-18 4 Klhdc1 +Ank3 7.45084342823747e-21 1.66371011232963 0.84 0.119 6.90693185797614e-18 4 Ank3 +Dnahc7b 8.16724747676575e-21 2.95977071341094 1 0.296 7.57103841096185e-18 4 Dnahc7b +Susd3 9.97730457934355e-21 2.55913554287515 1 0.214 9.24896134505147e-18 4 Susd3 +Capn3 1.70183319442534e-20 1.22126594749743 0.76 0.099 1.57759937123229e-17 4 Capn3 +Siah2 2.00398615518644e-20 5.10580042818432 1 0.333 1.85769516585783e-17 4 Siah2 +Ahr 3.18514965344481e-20 2.14890321089539 0.88 0.152 2.95263372874334e-17 4 Ahr +Evl 5.27270534609733e-20 2.31645977821982 0.96 0.247 4.88779785583222e-17 4 Evl +Serpini11 1.35399622068809e-19 1.72843209712204 0.96 0.177 1.25515449657786e-16 4 Serpini1 +P2rx6 2.61666184508431e-19 0.950129972001398 0.68 0.07 2.42564553039316e-16 4 P2rx6 +Bnc2 3.94927011711101e-19 4.21307179261675 1 0.379 3.66097339856191e-16 4 Bnc2 +Ttc21b 4.48048445276014e-19 0.666020410145535 0.64 0.062 4.15340908770865e-16 4 Ttc21b +Dnahc8 5.22715420711798e-19 3.7400526030543 1 0.35 4.84557194999836e-16 4 Dnahc8 +Fut10 6.23018753154982e-19 2.07075648698933 0.92 0.21 5.77538384174668e-16 4 Fut10 +Lonrf2 6.34217074862136e-19 0.354172628499182 0.56 0.037 5.879192283972e-16 4 Lonrf2 +Tas1r2 7.04495979548227e-19 0.421965057952629 0.52 0.033 6.53067773041207e-16 4 Tas1r2 +Gm101 8.07028981530683e-19 0.263768382287443 0.48 0.025 7.48115865878944e-16 4 Gm101 +4430402I18Rik 9.54544352009576e-19 0.588769964434573 0.48 0.025 8.84862614312877e-16 4 4430402I18Rik +Rasl11b 1.09017706461955e-18 1.2719604565366 0.68 0.074 1.01059413890232e-15 4 Rasl11b +Dopey2 1.23412222064398e-18 2.46521496339263 1 0.292 1.14403129853697e-15 4 Dopey2 +Rab3d 6.97099089317303e-18 4.24009902346091 1 0.424 6.4621085579714e-15 4 Rab3d +Zfp461 9.54125850812601e-18 2.79391015742711 0.96 0.296 8.84474663703282e-15 4 Zfp46 +Tesc 1.42575894240167e-17 4.28319876026649 1 0.543 1.32167853960635e-14 4 Tesc +Gm48501 1.51070520726681e-17 2.99028675461912 0.88 0.148 1.40042372713633e-14 4 Gm4850 +Enox1 1.83316450470133e-17 2.6819020594255 0.96 0.288 1.69934349585813e-14 4 Enox1 +Pcolce2 1.86135141270605e-17 1.29751008542801 0.88 0.169 1.72547275957851e-14 4 Pcolce2 +Smox 2.13536172883873e-17 1.87779376131118 0.96 0.259 1.9794803226335e-14 4 Smox +Sema6a 2.14406962529618e-17 1.58284076135351 0.88 0.185 1.98755254264956e-14 4 Sema6a +Colq 2.3603500828545e-17 1.03980856383107 0.8 0.136 2.18804452680612e-14 4 Colq +Pkd2l2 2.71892984881251e-17 6.57367299331847 1 0.58 2.52044796984919e-14 4 Pkd2l2 +Gng12 5.20879562271918e-17 3.92418555424018 1 0.626 4.82855354226068e-14 4 Gng12 +Fam110b 5.45246622567631e-17 3.03441123299714 1 0.374 5.05443619120194e-14 4 Fam110b +Grip1 6.43222524165751e-17 3.00065060309105 0.96 0.379 5.96267279901651e-14 4 Grip1 +Sdcbp2 6.51561555010022e-17 2.49031673780251 0.96 0.28 6.0399756149429e-14 4 Sdcbp2 +Kbtbd8 9.15746574908903e-17 4.50107303384636 1 0.675 8.48897074940553e-14 4 Kbtbd8 +Smarca2 1.12135778373806e-16 3.78640779709216 1 0.547 1.03949866552518e-13 4 Smarca2 +Ryr31 1.44237139359135e-16 0.627514777502389 0.88 0.185 1.33707828185918e-13 4 Ryr3 +Angel2 1.82199871588075e-16 3.83080386011335 1 0.798 1.68899280962146e-13 4 Angel2 +Prdm16 2.68381093472491e-16 2.76162554974848 0.96 0.329 2.48789273648999e-13 4 Prdm16 +Lrrc27 3.16525223839145e-16 0.67519478929253 0.76 0.128 2.93418882498888e-13 4 Lrrc27 +Tnfaip8 5.13403829372961e-16 3.54092878529361 1 0.519 4.75925349828734e-13 4 Tnfaip8 +Wdr20a 6.4472674793875e-16 3.37979573290738 1 0.757 5.97661695339221e-13 4 Wdr20a +Dip2b 7.93025003718885e-16 2.46244970089408 1 0.918 7.35134178447407e-13 4 Dip2b +Gatad2a1 8.03925438308724e-16 2.01253895546818 1 0.996 7.45238881312187e-13 4 Gatad2a +Efcab3 8.96784868762304e-16 1.2165437446827 0.84 0.189 8.31319573342656e-13 4 Efcab3 +Trim401 9.21312485400265e-16 0.741336353862257 0.72 0.103 8.54056673966046e-13 4 Trim40 +Mthfd2 1.1900221590094e-15 3.44844450869168 1 0.765 1.10315054140172e-12 4 Mthfd2 +Samd4 1.22819332585726e-15 0.813572945963178 0.72 0.119 1.13853521306968e-12 4 Samd4 +St7 1.52639765700565e-15 2.34804539160805 0.92 0.305 1.41497062804424e-12 4 St7 +Ccdc501 1.73262684180119e-15 2.78236393233026 1 0.741 1.6061450823497e-12 4 Ccdc50 +Esrp1 2.15358595137848e-15 2.79025611469526 1 0.897 1.99637417692785e-12 4 Esrp1 +Epc1 2.44143143889722e-15 3.15231008010683 1 0.753 2.26320694385773e-12 4 Epc1 +Fnbp1l1 2.4849036132982e-15 2.55514054804515 1 0.827 2.30350564952743e-12 4 Fnbp1l +Laptm4b 2.75565270591397e-15 3.07446497583373 1 0.733 2.55449005838225e-12 4 Laptm4b +Ppp6r2 2.99049979396054e-15 0.99963316880588 0.88 0.202 2.77219330900142e-12 4 Ppp6r2 +Nfatc2 3.14349496883849e-15 0.965587073234795 0.68 0.111 2.91401983611328e-12 4 Nfatc2 +Wasl 3.48484666895757e-15 2.60436084458781 1 0.963 3.23045286212367e-12 4 Wasl +Sap130 4.71640712300202e-15 2.36507141567713 1 0.963 4.37210940302287e-12 4 Sap130 +Lrp121 5.23254850471444e-15 1.0591551206995 0.88 0.181 4.85057246387029e-12 4 Lrp12 +Lhpp 7.01638925672533e-15 1.46715675082804 0.84 0.181 6.50419284098438e-12 4 Lhpp +Ptprz1 7.03215254228908e-15 1.35543725846971 0.76 0.181 6.51880540670197e-12 4 Ptprz1 +Dtx3 7.25223184698049e-15 0.54392266592676 0.8 0.144 6.72281892215091e-12 4 Dtx3 +Clip21 7.80878858920451e-15 2.01339018920013 0.96 0.486 7.23874702219258e-12 4 Clip2 +Rtkn21 8.03399949755419e-15 1.26724988107886 1 0.305 7.44751753423273e-12 4 Rtkn2 +Hvcn1 1.12053546645201e-14 2.41789274166838 1 0.658 1.03873637740102e-11 4 Hvcn1 +Stau2 1.2367595864626e-14 2.07074698351048 0.96 0.387 1.14647613665083e-11 4 Stau2 +Plk4 1.33581451906097e-14 2.80283855306323 1 0.84 1.23830005916952e-11 4 Plk4 +Slc25a231 1.44439776190432e-14 2.13580735836247 1 0.494 1.33895672528531e-11 4 Slc25a23 +Pole41 2.11324493317209e-14 1.62699710846853 1 0.914 1.95897805305053e-11 4 Pole4 +Akap7 2.12831107436157e-14 2.57831943983047 1 0.687 1.97294436593318e-11 4 Akap7 +Tsc22d1 3.48261176531061e-14 2.63214857960689 1 0.86 3.22838110644293e-11 4 Tsc22d1 +Mfsd9 3.70578798646635e-14 0.862068552504602 0.68 0.115 3.43526546345431e-11 4 Mfsd9 +Akap6 4.54687996823394e-14 0.625701824653917 0.64 0.107 4.21495773055286e-11 4 Akap6 +Greb1 4.82986605512085e-14 0.415530438457458 0.64 0.103 4.47728583309703e-11 4 Greb1 +Smurf21 5.54519469152219e-14 2.61281359669241 0.96 0.905 5.14039547904107e-11 4 Smurf2 +Siah1b1 6.88384212800318e-14 2.53378500108403 1 0.761 6.38132165265894e-11 4 Siah1b +Rictor 8.33499404990563e-14 2.45152189375378 1 0.909 7.72653948426252e-11 4 Rictor +Gm165151 9.61612725379451e-14 2.51060028153012 1 0.86 8.91414996426751e-11 4 Gm16515 +Rbfox2 1.01694872453775e-13 2.88105291469517 1 0.819 9.42711467646492e-11 4 Rbfox2 +Lmln 1.4996227073163e-13 0.572766412339056 0.84 0.198 1.39015024968221e-10 4 Lmln +Cbfa2t3 1.63994150763106e-13 1.87750365403276 1 0.395 1.52022577757399e-10 4 Cbfa2t3 +Zbtb371 1.78031239010418e-13 2.10174574109439 0.96 0.428 1.65034958562657e-10 4 Zbtb37 +Mapk9 1.8386646085678e-13 2.28596952315469 0.96 0.741 1.70444209214235e-10 4 Mapk9 +Fbxo8 2.68575165241775e-13 2.4653824779672 0.96 0.815 2.48969178179126e-10 4 Fbxo8 +Donson1 2.80940463809226e-13 2.33381660718263 0.96 0.72 2.60431809951153e-10 4 Donson +Clec12a 3.77654698675618e-13 0.364306959985906 0.44 0.041 3.50085905672298e-10 4 Clec12a +Fbxo18 4.45324365806014e-13 2.27781203571058 1 0.7 4.12815687102175e-10 4 Fbxo18 +Ankrd521 4.67252387989619e-13 2.54739802783053 0.96 0.617 4.33142963666377e-10 4 Ankrd52 +Myo18a 6.11141165268913e-13 2.06844544934556 1 0.646 5.66527860204282e-10 4 Myo18a +Epb4.11 1.21447020068671e-12 1.81256051702273 1 0.922 1.12581387603658e-09 4 Epb4.1 +Usp44 1.28594907519433e-12 0.416002153793656 0.52 0.066 1.19207479270515e-09 4 Usp44 +Ccdc14 1.36708521132431e-12 2.79257996761963 1 0.708 1.26728799089764e-09 4 Ccdc14 +Adam7 1.4203976051265e-12 0.348439639382281 0.32 0.016 1.31670857995227e-09 4 Adam7 +Mtf11 1.51333151192486e-12 1.78489692061191 1 0.938 1.40285831155434e-09 4 Mtf1 +Rab3gap1 1.54558863715183e-12 2.42886177852512 1 0.947 1.43276066663975e-09 4 Rab3gap1 +Lin541 1.70591357026912e-12 2.2921828152613 0.96 0.815 1.58138187963947e-09 4 Lin54 +Manba 2.04546019977721e-12 1.96460067226587 0.92 0.313 1.89614160519348e-09 4 Manba +Nfkbiz 2.45636907813087e-12 0.304652213230019 0.84 0.181 2.27705413542732e-09 4 Nfkbiz +Arfgef1 2.53851581248402e-12 2.1587347528686 1 0.914 2.35320415817268e-09 4 Arfgef1 +Drosha 3.0515306554585e-12 1.69972069432367 1 0.955 2.82876891761003e-09 4 Drosha +Duoxa2 3.41008561799742e-12 4.10048214723455 0.6 0.111 3.16114936788361e-09 4 Duoxa2 +Whsc1 3.94791321253577e-12 2.0060275070671 1 0.757 3.65971554802066e-09 4 Whsc1 +Phf7 5.2538641350301e-12 1.0000241645655 0.96 0.325 4.8703320531729e-09 4 Phf7 +Ccdc88a 5.98916505562513e-12 2.42179057840329 0.96 0.617 5.5519560065645e-09 4 Ccdc88a +Abca131 7.00771139114867e-12 1.82515120980123 1 0.588 6.49614845959482e-09 4 Abca13 +AI314180 9.95101592108729e-12 1.55419750334187 0.96 0.967 9.22459175884792e-09 4 AI314180 +Slc2a9 9.95573777635433e-12 0.531905133491423 0.72 0.165 9.22896891868046e-09 4 Slc2a9 +Usp541 9.99899983988007e-12 1.79930950344482 0.96 0.782 9.26907285156882e-09 4 Usp54 +1810041L15Rik 1.11515763120716e-11 0.354107484394614 0.4 0.037 1.03375112412903e-08 4 1810041L15Rik +Ypel51 1.53245639830212e-11 2.06164855835124 1 0.975 1.42058708122606e-08 4 Ypel5 +Ube2w 1.80822603509713e-11 1.5822011196932 1 0.802 1.67622553453504e-08 4 Ube2w +Rnf19a 1.95458410371035e-11 2.06236504513621 0.96 0.63 1.81189946413949e-08 4 Rnf19a +Mllt41 2.10213656370971e-11 1.29056444719059 1 0.971 1.9486805945589e-08 4 Mllt4 +Neb 2.42859221289881e-11 1.0054431864365 0.96 0.383 2.2513049813572e-08 4 Neb +Ces2a 2.9598637940942e-11 0.528602459347014 0.48 0.07 2.74379373712532e-08 4 Ces2a +Pum22 5.07846311659841e-11 1.26577449997296 1 1 4.70773530908673e-08 4 Pum2 +Lin28a1 9.16303545779576e-11 1.97837541344865 1 0.774 8.49413386937667e-08 4 Lin28a +Ammecr1l1 1.0595642318885e-10 1.30069913158308 1 0.934 9.8221604296064e-08 4 Ammecr1l +Hspa1a1 1.17018303498107e-10 1.42269894187353 0.88 0.263 1.08475967342745e-07 4 Hspa1a +Homer1 1.20704064467784e-10 1.49317057034198 0.96 0.576 1.11892667761636e-07 4 Homer1 +Diras1 1.3630235001043e-10 0.415276424024409 0.32 0.025 1.26352278459669e-07 4 Diras1 +Cd101 1.70283592326964e-10 0.294664194949653 0.44 0.058 1.57852890087095e-07 4 Cd101 +Tcfe3 1.89478508653221e-10 1.99798369196135 1 0.757 1.75646577521536e-07 4 Tcfe3 +Mapk8ip3 2.14705209782319e-10 1.75575866634819 1 0.605 1.99031729468209e-07 4 Mapk8ip3 +Kif14 3.18654598247209e-10 1.7836457907186 0.96 0.831 2.95392812575163e-07 4 Kif14 +Siah1a1 3.59306799284511e-10 1.68240494757085 1 0.798 3.33077402936742e-07 4 Siah1a +Cdca41 4.75101589767026e-10 1.3955524461087 0.96 0.922 4.40419173714033e-07 4 Cdca4 +Dda11 5.76898794315175e-10 1.3965019853191 1 0.905 5.34785182330168e-07 4 Dda1 +Chd6 8.03854949506152e-10 1.66944336822125 1 0.827 7.45173538192203e-07 4 Chd6 +Gsdmc31 1.46906905317228e-09 0.57584832518055 0.88 0.321 1.3618270122907e-06 4 Gsdmc3 +Apitd11 1.71324421721923e-09 1.12058340834234 1 0.909 1.58817738936223e-06 4 Apitd1 +Tbc1d14 1.93074772294136e-09 1.92716796676189 1 0.856 1.78980313916664e-06 4 Tbc1d14 +Zfp300 2.13925426442828e-09 0.690280158516252 0.36 0.041 1.98308870312501e-06 4 Zfp300 +Etv1 2.53369955736004e-09 0.292607851542103 0.76 0.247 2.34873948967276e-06 4 Etv1 +Gal3st21 2.9895098628407e-09 1.92318013917008 0.72 0.206 2.77127564285333e-06 4 Gal3st2 +Dnaja21 3.5912080601965e-09 0.952901723107821 1 0.996 3.32904987180216e-06 4 Dnaja2 +Pla2g6 5.17503207813425e-09 1.37297895385903 0.96 0.543 4.79725473643045e-06 4 Pla2g6 +Spred2 5.76272075500298e-09 0.809905853501114 0.96 0.449 5.34204213988776e-06 4 Spred2 +Dand5 9.91338209094858e-09 0.403634528108972 0.72 0.189 9.18970519830933e-06 4 Dand5 +Lnpep1 1.16247943986125e-08 1.17947704258048 0.96 0.584 1.07761844075138e-05 4 Lnpep +4930519G04Rik 1.425712336594e-08 0.327728611789388 0.6 0.169 1.32163533602264e-05 4 4930519G04Rik +Ccnt2 1.57787540875492e-08 1.37863786771065 0.96 0.893 1.46269050391581e-05 4 Ccnt2 +B230120H23Rik1 1.85023251584262e-08 0.668096996919293 0.92 0.519 1.71516554218611e-05 4 B230120H23Rik +Usp371 2.37372869856658e-08 0.944540846473084 0.96 0.975 2.20044650357122e-05 4 Usp37 +Ip6k21 2.88140024893256e-08 2.31458308917773 0.96 0.588 2.67105803076048e-05 4 Ip6k2 +Tinf21 3.03632343670193e-08 1.17477979947318 1 0.885 2.81467182582269e-05 4 Tinf2 +Scn1a 7.76813552061107e-08 0.457526138908355 0.64 0.267 7.20106162760646e-05 4 Scn1a +Arid5a1 8.89336573899189e-08 1.96177002911922 0.84 0.337 8.24415004004548e-05 4 Arid5a +Prkca 1.11188275098875e-07 0.250671766730116 0.4 0.07 0.000103071531016657 4 Prkca +Lcor 1.52910814008632e-07 0.892594653434745 1 0.531 0.000141748324586002 4 Lcor +2310008H04Rik 1.99158752567749e-07 1.12743725664549 0.96 0.597 0.000184620163630303 4 2310008H04Rik +Rbl11 2.27732554243415e-07 0.905408812201592 0.96 0.601 0.000211108077783645 4 Rbl1 +Mid1ip11 2.3144668676797e-07 2.13440314618512 0.72 0.288 0.000214551078633908 4 Mid1ip1 +Bcl2l131 2.43810414218465e-07 0.977553347709759 1 0.955 0.000226012253980517 4 Bcl2l13 +Il15 3.61625614654534e-07 0.430016785401643 0.32 0.049 0.000335226944784753 4 Il15 +Slc16a13 3.87854430460621e-07 1.26838747800073 0.92 0.469 0.000359541057036995 4 Slc16a13 +Mgat4a1 4.3081640741542e-07 0.882005002652121 1 0.802 0.000399366809674095 4 Mgat4a +Hist1h1a 4.42696168110822e-07 1.52576619380862 1 0.914 0.000410379347838732 4 Hist1h1a +Slc35c11 4.4465413429829e-07 1.53509566458281 0.88 0.626 0.000412194382494515 4 Slc35c1 +Rasd21 1.02542329381111e-06 0.312486842131605 0.6 0.177 0.000950567393362897 4 Rasd2 +6720489N17Rik1 1.07287949412387e-06 1.73563711321024 0.96 0.967 0.00099455929105283 4 6720489N17Rik +Trip111 1.17107629306268e-06 0.86751998372811 1 0.765 0.0010855877236691 4 Trip11 +Zcchc81 1.23923297111951e-06 1.37577004828821 0.96 0.979 0.00114876896422779 4 Zcchc8 +D19Ertd737e 1.33656742477104e-06 0.818070859921239 1 0.835 0.00123899800276276 4 D19Ertd737e +Tcf3 1.47341707954375e-06 0.698594064666665 0.96 0.811 0.00136585763273706 4 Tcf3 +Ccdc115 1.59108696515693e-06 0.935789171059449 1 0.942 0.00147493761670047 4 Ccdc115 +Sec14l1 2.22515999218069e-06 0.441003772850919 0.96 0.547 0.0020627233127515 4 Sec14l1 +Gpatch31 2.28602215776352e-06 1.71564636112472 0.84 0.37 0.00211914254024678 4 Gpatch3 +1700029F12Rik 3.16670921538127e-06 1.25920332789257 0.6 0.206 0.00293553944265843 4 1700029F12Rik +D1Bwg0212e 3.54092462883736e-06 1.09075409376934 0.96 0.819 0.00328243713093223 4 D1Bwg0212e +Agbl5 3.63234366845022e-06 0.359000375003823 0.88 0.51 0.00336718258065336 4 Agbl5 +Kif91 4.01899120973089e-06 0.768464087196651 0.88 0.403 0.00372560485142053 4 Kif9 +Ctnna2 4.18835867427856e-06 0.489080438185307 0.4 0.107 0.00388260849105622 4 Ctnna2 +Traf7 4.59597118765464e-06 0.70767916224615 1 0.959 0.00426046529095585 4 Traf7 +Rbm22 5.36974645549668e-06 0.730087432476789 1 0.992 0.00497775496424542 4 Rbm22 +Rspry11 5.69095110889555e-06 1.0141365217818 0.96 0.716 0.00527551167794617 4 Rspry1 +Mecp2 6.73951105806661e-06 0.990901622242648 0.88 0.551 0.00624752675082775 4 Mecp2 +Ogfrl1 7.83911040043734e-06 0.426596561676906 0.96 0.56 0.00726685534120541 4 Ogfrl1 +Nmb1 8.1467937980205e-06 1.48728600328544 1 0.728 0.007552077850765 4 Nmb +Nin2 8.41338109135364e-06 1.03986152957422 0.96 0.761 0.00779920427168482 4 Nin +Ccnyl1 8.75230930750994e-06 1.19543145693502 1 0.7 0.00811339072806172 4 Ccnyl1 +Tex14 9.56222447108374e-06 0.494746429430875 0.84 0.436 0.00886418208469463 4 Tex14 +St5 1.14940659749145e-05 0.605165682719874 1 0.638 0.0106549991587457 4 St5 +Nbeal1 1.21823749551211e-05 0.832173404655711 0.96 0.897 0.0112930615833972 4 Nbeal1 +Clk21 1.68162380954407e-05 1.21176749980517 0.96 0.852 0.0155886527144735 4 Clk2 +Pip5k1c 1.80263888169973e-05 0.716186824000705 0.96 0.757 0.0167104624333565 4 Pip5k1c +Tmem87b1 1.81967024576279e-05 0.686361617836365 1 0.835 0.016868343178221 4 Tmem87b +Ercc4 2.93090146915522e-05 1.22254679642911 1 0.877 0.0271694566190689 4 Ercc4 +Alox121 2.9986865925419e-05 0.814366019417343 0.96 0.691 0.0277978247128634 4 Alox12 +Cotl1 3.55238391783376e-05 0.291812126661166 0.8 0.387 0.032930598918319 4 Cotl1 +Vps39 3.62481073948892e-05 1.28853126628222 0.96 0.827 0.0336019955550623 4 Vps39 +4632434I11Rik1 3.93389287722145e-05 0.608031235714694 0.96 0.934 0.0364671869718429 4 4632434I11Rik +Ankrd27 4.13605244951355e-05 0.78336551232952 1 0.794 0.0383412062069906 4 Ankrd27 +Fah1 4.76477821526752e-05 0.331144383476058 0.4 0.107 0.0441694940555299 4 Fah +Zmym4 4.99487631936679e-05 0.819479010245981 0.96 0.93 0.0463025034805301 4 Zmym4 +Mosc21 8.75878249805554e-05 0.804360337949048 0.96 0.753 0.0811939137569749 4 Mosc2 +Fem1c1 0.000134144950945859 1.59351176629955 0.96 0.831 0.124352369526812 4 Fem1c +D4Bwg0951e1 0.000137801588617095 0.565645554404937 0.8 0.403 0.127742072648047 4 D4Bwg0951e +Zkscan141 0.00014549216540626 0.583843128566121 0.92 0.576 0.134871237331603 4 Zkscan14 +Cry21 0.000155364520126801 0.42931037311356 0.92 0.531 0.144022910157544 4 Cry2 +Dtnb1 0.000163437118936719 0.485702200066726 1 0.7 0.151506209254338 4 Dtnb +Abcc32 0.000168288248321098 0.250119026164717 0.88 0.514 0.156003206193658 4 Abcc3 +Zfp523 0.000191398072795126 0.329049002394344 0.36 0.107 0.177426013481082 4 Zfp523 +Sec31a 0.000344008370420095 0.924496462911904 1 0.984 0.318895759379428 4 Sec31a +Ercc5 0.000413521809768657 0.419204737728817 0.88 0.584 0.383334717655545 4 Ercc5 +Tnrc6a 0.000536560574620653 0.406801300987023 0.96 0.988 0.497391652673345 4 Tnrc6a +Ctnnd1 0.000892942115112949 0.766388544590886 1 0.984 0.827757340709703 4 Ctnnd1 +Zmym31 0.00106377539780854 0.443295470931702 1 0.815 0.986119793768515 4 Zmym3 +Zfp8301 0.00119573195456822 0.556755544900666 1 0.889 1 4 Zfp830 +Hells1 0.00123148933789219 0.320858221286585 0.96 0.979 1 4 Hells +Nlrp31 0.00167546658564824 0.682913638083824 0.48 0.23 1 4 Nlrp3 +Serpine21 0.00170095741538562 0.492169327022354 0.96 0.757 1 4 Serpine2 +Ttll5 0.00173194686095845 0.334901585350436 0.96 0.823 1 4 Ttll5 +Shprh 0.00223213166460002 0.455600408375772 0.96 0.881 1 4 Shprh +Dcdc2c1 0.00228198449889257 1.55885090391374 0.84 0.675 1 4 Dcdc2c
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_out.tsv Fri Jul 07 01:43:02 2023 +0000 @@ -0,0 +1,103 @@ +p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene +1.67295292546245e-13 0.326405715743977 1 1 2.17483880310118e-12 1 CD3 +1.5642098215071e-44 0.495970381707604 1 1 2.03347276795923e-43 3 CD3 +1.14196527784025e-35 0.40085553451009 1 1 1.48455486119233e-34 3 CD4 +1.00171227157907e-42 0.49278398824099 1 1 1.30222595305279e-41 4 CD3 +4.45804690128427e-32 0.383908885768934 1 1 5.79546097166956e-31 4 CD4 +2.3270323108152e-64 0.535858744002285 1 1 3.02514200405976e-63 6 CD11c +4.59697497155158e-71 0.582642681231806 1 1 5.97606746301705e-70 8 CD11c +5.42829982399312e-23 0.310022335647084 1 1 7.05678977119106e-22 9 CD11c +5.34022845897306e-70 0.60889940093635 1 1 6.94229699666497e-69 10 CD11c +1.94515080115917e-75 0.987231181827462 1 1 2.52869604150692e-74 11 CD19 +1.3401718411323e-32 0.27534720926661 1 1 1.74222339347199e-31 11 CD45RA +6.82783507401538e-62 0.57275793552547 1 1 8.87618559621999e-61 12 CD11c +2.04431843457248e-31 0.449927697936415 1 1 2.65761396494422e-30 15 CD11c +3.39342323568419e-26 0.404810867237044 1 1 4.41145020638945e-25 16 CD11c +7.88511793517547e-29 0.465776338611985 1 1 1.02506533157281e-27 17 CD11c +1.91570514633727e-46 0.56726960905273 1 1 2.49041669023845e-45 18 CD11c +5.1260483533881e-82 1.18155234784116 1 1 6.66386285940453e-81 20 CD8 +1.57361935775751e-47 0.391899061098195 1 1 2.04570516508476e-46 20 CD45RA +8.74284608877472e-39 0.546627661446195 1 1 1.13656999154071e-37 23 CD11c +1.96816328438562e-27 0.525377309779508 1 1 2.55861226970131e-26 24 CD3 +2.80113243084789e-26 0.445779372516199 1 1 3.64147216010226e-25 24 CD4 +2.08891825701061e-32 0.359032672171917 1 1 2.71559373411379e-31 25 CD45RA +6.38184609794435e-23 0.314402863729703 1 1 8.29639992732766e-22 25 CD56 +2.33924416208311e-19 0.275395941678534 1 1 3.04101741070804e-18 25 CD16 +1.23100762344444e-72 0.527654790808374 1 1 1.60030991047777e-71 26 CD45RA +1.00222124580754e-61 0.47303501407078 1 1 1.3028876195498e-60 26 CD56 +5.04433216574995e-61 0.499525696517984 1 1 6.55763181547493e-60 26 CD16 +2.57942814886754e-19 0.397056393594097 1 1 3.3532565935278e-18 26 CD8 +3.80436056159182e-21 0.471090809116061 1 1 4.94566873006937e-20 27 CD3 +5.62262803624727e-14 0.365368408368207 1 1 7.30941644712145e-13 27 CD4 +8.05030043675788e-29 0.556377398183442 1 1 1.04653905677852e-27 28 CD3 +5.68183022990689e-24 0.462604140851 1 1 7.38637929887895e-23 28 CD4 +4.32372215869929e-27 0.492374012295227 1 1 5.62083880630908e-26 30 CD4 +8.80072296811784e-27 0.562209188025505 1 1 1.14409398585532e-25 30 CD3 +5.86102527405308e-30 0.514318772298818 1 1 7.619332856269e-29 31 CD4 +1.10478058693055e-26 0.551831262152829 1 1 1.43621476300972e-25 31 CD3 +6.38562416996792e-11 0.407403482613083 1 1 8.30131142095829e-10 32 CD3 +4.17895569544475e-06 0.272549702717712 1 1 5.43264240407818e-05 32 CD4 +3.72341120344556e-39 0.63404032335664 1 1 4.84043456447923e-38 33 CD11c +3.47626583425057e-31 0.298415769867169 1 1 4.51914558452574e-30 33 CD14 +1.61092774622993e-19 0.32674447986965 1 1 2.09420607009891e-18 35 CD45RA +7.8712241758892e-27 0.572421953528271 1 1 1.0232591428656e-25 36 CD11c +2.53970993841925e-22 0.278363837640406 1 1 3.30162291994503e-21 36 CD14 +1.35360047893276e-42 1.32718688149546 1 1 1.75968062261259e-41 37 CD8 +5.24757172988244e-13 0.263336896623814 1 1 6.82184324884717e-12 37 CD45RA +0.00411967300711807 0.251455582065055 1 1 0.0535557490925349 37 CD3 +5.08213840057668e-09 0.388143218090763 1 1 6.60677992074969e-08 38 CD3 +5.78899385075161e-07 0.325099136996257 1 1 7.52569200597709e-06 38 CD4 +4.66505722311064e-22 0.586604170424365 1 1 6.06457439004383e-21 39 CD3 +3.76660069557731e-21 0.514611202436318 1 1 4.8965809042505e-20 39 CD4 +5.55663908351586e-38 0.515577202059993 1 1 7.22363080857062e-37 40 CD45RA +6.27348968932591e-32 0.472480692520507 1 1 8.15553659612369e-31 40 CD16 +1.42947043118412e-28 0.415013457906016 1 1 1.85831156053936e-27 40 CD56 +1.8793375763755e-14 0.352665542997354 1 1 2.44313884928815e-13 40 CD8 +5.6008185645827e-24 0.602331877466961 1 1 7.2810641339575e-23 41 CD11c +2.57123247695116e-20 0.285387697218841 1 1 3.34260222003651e-19 41 CD14 +1.49095077292205e-14 0.49697275611693 1 1 1.93823600479867e-13 43 CD4 +2.08946196531086e-14 0.555739574445692 1 1 2.71630055490412e-13 43 CD3 +2.19758957676378e-05 0.399823538718023 1 1 0.000285686644979291 44 CD3 +6.14864318795116e-05 0.326473015534509 1 1 0.00079932361443365 44 CD4 +1.27620616488274e-20 0.48718207480276 1 1 1.65906801434756e-19 46 CD45RA +5.73473851777945e-19 0.463918420273511 1 1 7.45516007311328e-18 46 CD16 +8.88217928924765e-16 0.402449826305318 1 1 1.15468330760219e-14 46 CD56 +3.86899212782144e-09 0.403347559498734 1 1 5.02968976616787e-08 46 CD8 +7.82441161756527e-14 0.54974339100417 1 1 1.01717351028348e-12 47 CD4 +1.64611664916494e-12 0.593590803126451 1 1 2.13995164391443e-11 47 CD3 +1.50261128404362e-08 0.444698278386498 1 1 1.9533946692567e-07 48 CD4 +3.0693920280249e-08 0.485806405732138 1 1 3.99020963643237e-07 48 CD3 +3.75064021004935e-05 0.426060220487989 1 1 0.000487583227306415 49 CD3 +0.000142612327520314 0.368345962674295 1 1 0.00185396025776409 49 CD4 +1.75303069982881e-08 0.553523232257216 1 1 2.27893990977745e-07 50 CD3 +2.92205657488682e-07 0.472836909811648 1 1 3.79867354735287e-06 50 CD4 +1.58132516634947e-07 0.546611394241725 1 1 2.05572271625431e-06 52 CD3 +1.9461168179332e-07 0.488063324884708 1 1 2.52995186331316e-06 52 CD4 +8.03593559106167e-08 0.569767489448342 1 1 1.04467162683802e-06 54 CD3 +1.06870991801859e-06 0.487932704728795 1 1 1.38932289342417e-05 54 CD4 +0.000814556186990549 0.351686671472014 1 1 0.0105892304308771 56 CD3 +2.51009951330222e-06 0.493665228200334 1 1 3.26312936729289e-05 57 CD4 +2.42776604502913e-05 0.523629664434363 1 1 0.000315609585853786 57 CD3 +5.42134770798451e-06 0.496080353437594 1 1 7.04775202037986e-05 58 CD4 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_out.tsv Fri Jul 07 01:43:02 2023 +0000 @@ -0,0 +1,582 @@ +p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene +0 6.05663691346878 1 0.014 0 0 CD9 +1.9822323994606e-32 0.892085602138872 0.845 0.67 5.33220515454903e-30 0 CD74 +1.15168092712414e-08 0.478645233478619 0.323 0.19 3.09802169396393e-06 0 CD36 +2.8479031688574e-07 0.475224325321269 0.342 0.22 7.66085952422642e-05 0 CD68 +1.19367791108326e-06 0.319116267570157 0.356 0.236 0.000321099358081397 0 CD14 +1.25526626910762e-300 2.55646528238641 0.997 0.174 3.37666626389951e-298 1 CD247 +4.9467417746979e-104 1.38113679016585 1 0.491 1.33067353739374e-101 1 CD7 +3.26887578464599e-22 0.738081621550979 0.711 0.447 8.79327586069771e-20 1 CD3D +1.67975517808425e-21 0.6897744848159 0.646 0.375 4.51854142904665e-19 1 CD3E +5.06329852867774e-18 0.772122890497265 0.523 0.295 1.36202730421431e-15 1 CD3G +1.27114026491996e-14 0.540176080901698 0.729 0.537 3.41936731263469e-12 1 CD69 +4.22106923632502e-12 0.628229473292235 0.431 0.256 1.13546762457143e-09 1 CD27 +1.59191271885828e-09 0.923324279812694 0.28 0.161 4.28224521372878e-07 1 CD96 +6.33331731091395e-06 0.635612480130467 0.3 0.202 0.00170366235663585 1 CD2 +1.2084710019556e-05 0.652639529253708 0.266 0.176 0.00325078699526057 1 AAK1 +7.18353005289289e-05 0.45395573069296 0.36 0.264 0.0193236958422819 1 CDC42SE2 +0 7.28866683945211 1 0.01 0 2 CDC34 +6.2438029160881e-11 0.287473417951871 0.837 0.671 1.6795829844277e-08 2 CD74 +1.67553729019084e-291 2.5252687279094 1 0.161 4.50719531061337e-289 3 CDC42SE1 +1.81222647838563e-48 0.774911191999161 1 0.494 4.87488922685735e-46 3 CD7 +1.59722179115194e-38 0.979326889347329 0.758 0.372 4.29652661819873e-36 3 CD3E +7.84242124211886e-35 0.885592128425985 0.81 0.444 2.10961131412997e-32 3 CD3D +1.99915714824053e-33 1.11040695652189 0.611 0.293 5.37773272876704e-31 3 CD3G +2.3333724887806e-29 1.01503304498776 0.549 0.252 6.27677199481982e-27 3 CD27 +1.04002760149565e-21 0.661402834305967 0.833 0.534 2.79767424802329e-19 3 CD69 +2.11673614992016e-20 0.44565536712769 0.961 0.849 5.69402024328522e-18 3 CD52 +4.16399404112572e-16 1.17812983627874 0.261 0.108 1.12011439706282e-13 3 CD6 +6.12847805829085e-12 0.906143067361228 0.307 0.156 1.64856059768024e-09 3 CCR7 +3.64114850082905e-09 0.669170386110504 0.346 0.2 9.79468946723015e-07 3 CD2 +4.14796430174784e-09 0.753573810220556 0.294 0.161 1.11580239717017e-06 3 CD96 +1.5417100566513e-06 0.656281233809736 0.284 0.175 0.0004147200052392 3 AAK1 +3.81221452867488e-06 0.523887078268232 0.382 0.264 0.00102548570821354 3 CDC42SE2 +3.97949109644182e-05 0.443250782597945 0.379 0.271 0.0107048310494285 3 CCT3 +0.000406152806467521 0.369291108612562 0.376 0.279 0.109255104939763 3 CCT4 +2.86179772528272e-140 1.69823655981722 1 0.494 7.69823588101052e-138 4 CD7 +5.75083718491135e-41 1.12108078531178 0.734 0.373 1.54697520274115e-38 4 CD3E +2.87854133026334e-40 0.975825622716567 0.826 0.444 7.74327617840839e-38 4 CD3D +3.21739743549182e-23 0.915070086700084 0.566 0.294 8.65479910147299e-21 4 CD3G +1.07571393161663e-22 0.703404470988817 0.809 0.535 2.89367047604873e-20 4 CD69 +5.66376326372948e-21 0.998065485935792 0.493 0.254 1.52355231794323e-18 4 CD27 +5.60713087816813e-17 0.410160383521315 0.967 0.849 1.50831820622723e-14 4 CD52 +5.74774963343849e-14 1.097599612095 0.309 0.156 1.54614465139495e-11 4 CCR7 +4.99928644683509e-12 0.95149999528962 0.355 0.2 1.34480805419864e-09 4 CD2 +7.61741524350528e-07 0.566723778496881 0.388 0.27 0.000204908470050292 4 CCT3 +0.00597813707088682 0.325303001531855 0.28 0.217 1 4 CCT2 +0 6.3624837958636 1 0.012 0 5 ABCB7 +0 3.58747133818528 0.88 0.073 0 6 ABI3 +1.42748858021799e-58 1.53828071963406 0.634 0.212 3.83994428078639e-56 6 CD68 +1.07762676060828e-50 1.09102064840927 0.942 0.669 2.89881598603628e-48 6 CD74 +5.07731529501781e-32 1.3974890987987 0.33 0.1 1.36579781435979e-29 6 CD86 +6.97336181247085e-29 1.45563803514765 0.293 0.088 1.87583432755466e-26 6 CD300E +6.62536629976547e-23 0.979237343350899 0.507 0.232 1.78222353463691e-20 6 CD14 +1.29879352423192e-22 1.43741112294113 0.264 0.088 3.49375458018387e-20 6 CD83 +1.6407031418007e-16 0.644133693508753 0.409 0.189 4.41349145144389e-14 6 CD36 +3.0445113820671e-05 0.349068488613858 0.714 0.589 0.00818973561776051 6 CDC42 +6.55583677910468e-261 2.71000373077191 1 0.165 1.76352009357916e-258 7 CDC42SE1 +1.29143089025351e-75 2.20661973642783 0.428 0.088 3.47394909478194e-73 7 ABI3 +1.2548958759207e-31 1.71962975512911 0.28 0.078 3.37566990622669e-29 7 CD160 +5.19152613393742e-13 0.878068535710515 0.387 0.202 1.39652053002917e-10 7 CD247 +1.10840324003048e-07 0.361221713958942 0.587 0.394 2.98160471568199e-05 7 CD63 +2.21746335078764e-07 0.483423824732453 0.723 0.589 5.96497641361876e-05 7 CDC42 +7.99517400666954e-06 0.421396504601738 0.351 0.221 0.00215070180779411 7 CD68 +6.76789013958815e-05 0.533330797898812 0.347 0.243 0.0182056244754921 7 CD97 +0.0016339913122411 0.339035260828892 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