Mercurial > repos > iuc > multigsea
changeset 0:28e29a3d0eda draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
| author | iuc |
|---|---|
| date | Wed, 07 Jun 2023 19:48:50 +0000 |
| parents | |
| children | e48b10ce08b8 |
| files | macros.xml multiGSEA.R multigsea.xml test-data/metabolome.tsv test-data/proteome.tsv test-data/transcriptome.tsv |
| diffstat | 6 files changed, 28842 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,42 @@ +<macros> + <token name="@TOOL_VERSION@">1.8.0</token> + <token name="@SUFFIX_VERSION@">0</token> + <token name="@PROFILE@">20.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-multigsea</requirement> + <requirement type="package" version="2.2.1">r-argparse</requirement> + <requirement type="package" version="1.0.0">bioconductor-metaboliteidmapping</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Hs.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Mm.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Rn.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Cf.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Bt.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Ss.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Gg.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Xl.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Dr.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Dm.eg.db</requirement> + <requirement type="package" version="3.16.0">bioconductor-org.Ce.eg.db</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">doi:10.1186/s12859-020-03910-x.</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">multiGSEA</xref> + </xrefs> + </xml> + <xml name="macro_IDs" tokens="name,label"> + <param name="@NAME@" type="select" label="@LABEL@"> + <option value="SYMBOL">SYMBOL</option> + <option value="ENTREZID">ENTREZID</option> + <option value="UNIPROT">UNIPROT</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="REFSEQ">REFSEQ</option> + </param> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiGSEA.R Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,172 @@ +library(multiGSEA, + quietly = TRUE, + warn.conflicts = FALSE) +library(argparse, quietly = TRUE, warn.conflicts = FALSE) + +################################################################################ +### Input Processing +################################################################################ + + +# Collect arguments from command line +parser <- ArgumentParser(description = "multiGSEA R script") + +parser$add_argument("--transcriptomics", required = FALSE, + help = "Transcriptomics data") +parser$add_argument( + "--transcriptome_ids", + required = FALSE, + help = "Transcriptomics ids", + default = "SYMBOL" +) +parser$add_argument("--proteomics", required = FALSE, + help = "Proteomics data") +parser$add_argument( + "--proteome_ids", + required = FALSE, + help = "Proteomics ids", + default = "SYMBOL" +) +parser$add_argument("--metabolomics", required = FALSE, + help = "Metabolomics data") +parser$add_argument( + "--metabolome_ids", + required = FALSE, + help = "Metabolomics ids", + default = "HMDB" +) +parser$add_argument("--organism", required = TRUE, + help = "Organism") +parser$add_argument("--combine_pvalues", required = TRUE, + help = "Combine p-values method") +parser$add_argument("--padj_method", required = TRUE, + help = "P-adjustment method") +parser$add_argument("--databases", + required = TRUE, + help = "Pathway databases") + +args <- parser$parse_args() + +## ----Load library------------------------------------------------------------- + +organism_mapping <- c( + "hsapiens" = "org.Hs.eg.db", + "mmusculus" = "org.Mm.eg.db", + "rnorvegicus" = "org.Rn.eg.db", + "cfamiliaris" = "org.Cf.eg.db", + "btaurus" = "org.Bt.eg.db", + "sscrofa" = "org.Ss.eg.db", + "ggallus" = "org.Gg.eg.db", + "drerio" = "org.Xl.eg.db", + "xlaevis" = "org.Dr.eg.db", + "dmelanogaster" = "org.Dm.eg.db", + "celegans" = "org.Ce.eg.db" +) + +library(organism_mapping[args$organism], character.only = TRUE) + + +## ----Load omics data---------------------------------------------------------- + +layer <- c() + +if (!is.null(args$transcriptomics)) { + transcriptome <- read.csv( + args$transcriptomics, + header = TRUE, + sep = "\t", + dec = "." + ) + layer <- append(layer, "transcriptome") +} + +if (!is.null(args$proteomics)) { + proteome <- read.csv(args$proteomics, + header = TRUE, + sep = "\t", + dec = ".") + layer <- append(layer, "proteome") +} + +if (!is.null(args$metabolomics)) { + metabolome <- read.csv(args$metabolomics, + header = TRUE, + sep = "\t", + dec = ".") + layer <- append(layer, "metabolome") +} + +## ----rank_features------------------------------------------------------------ + +# create data structure +omics_data <- initOmicsDataStructure(layer) + +## add transcriptome layer +if (!is.null(args$transcriptomics)) { + omics_data$transcriptome <- rankFeatures(transcriptome$logFC, + transcriptome$pValue) + names(omics_data$transcriptome) <- transcriptome$Symbol +} + +## add proteome layer +if (!is.null(args$proteomics)) { + omics_data$proteome <- rankFeatures(proteome$logFC, proteome$pValue) + names(omics_data$proteome) <- proteome$Symbol +} + +## add metabolome layer +## HMDB features have to be updated to the new HMDB format +if (!is.null(args$metabolomics)) { + omics_data$metabolome <- + rankFeatures(metabolome$logFC, metabolome$pValue) + names(omics_data$metabolome) <- metabolome$HMDB + names(omics_data$metabolome) <- gsub("HMDB", "HMDB00", + names(omics_data$metabolome)) +} + + +## remove NA's and sort feature ranks +omics_data <- lapply(omics_data, function(vec) { + sort(vec[!is.na(vec)]) +}) + +## ----Pathway definitions------------------------------------------------------ + +pathways <- + getMultiOmicsFeatures( + dbs = unlist(strsplit(args$databases, ",", fixed = TRUE)), + layer = layer, + returnTranscriptome = args$transcriptome_ids, + returnProteome = args$proteome_ids, + returnMetabolome = args$metabolome_ids, + organism = args$organism, + useLocal = FALSE + ) + +## ----calculate enrichment----------------------------------------------------- + +enrichment_scores <- + multiGSEA(pathways, omics_data) + +## ----combine_pvalues---------------------------------------------------------- + +df <- extractPvalues(enrichmentScores = enrichment_scores, + pathwayNames = names(pathways[[1]])) + +df$combined_pval <- + combinePvalues(df, method = args$combine_pvalues) +df$combined_padj <- + p.adjust(df$combined_pval, method = args$padj_method) + +df <- cbind(data.frame(pathway = names(pathways[[1]])), df) + +## ----Write output------------------------------------------------------------- + +write.table( + df, + file = "results.tsv", + quote = FALSE, + sep = "\t", + col.names = TRUE, + row.names = FALSE +)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multigsea.xml Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,295 @@ +<tool id="multigsea" name="multiGSEA" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@"> + <description>GSEA-based pathway enrichment analysis for multi-omics data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro='requirements'/> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + </stdio> + <command><![CDATA[ + + Rscript '${__tool_directory__}/multiGSEA.R' + #if $transcriptomics_data.selector == "true" + --transcriptomics '${transcriptomics_data.transcriptomics}' + --transcriptome_ids $transcriptomics_data.transcriptome_ids + #end if + #if $proteomics_data.selector == "true" + --proteomics '${proteomics}' + --proteome_ids $proteomics_data.proteome_ids + #end if + #if $metabolomics_data.selector == "true" + --metabolomics '${metabolomics}' + --metabolome_ids $metabolomics_data.metabolome_ids + #end if + --organism $organism + --databases $databases + --combine_pvalues $combine_pvalues + --padj_method $padj_method + + ]]></command> + <inputs> + <conditional name="transcriptomics_data"> + <param name="selector" type="select" label="Select transcriptomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="transcriptomics" type="data" format="tabular" label="Transcriptomics data" + help="String specifying the returned gene ID format." /> + <expand macro="macro_IDs" name="transcriptome_ids" label="Gene ID format in transcriptomics data"/> + </when> + <when value="false"/> + </conditional> + <conditional name="proteomics_data"> + <param name="selector" type="select" label="Select proteomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="proteomics" type="data" format="tabular" label="Proteomics data" + help="String specifying the returned gene ID format" /> + <expand macro="macro_IDs" name="proteome_ids" label="Gene ID format in proteomics data"/> + </when> + <when value="false"/> + </conditional> + <conditional name="metabolomics_data"> + <param name="selector" type="select" label="Select metabolomics data"> + <option value="true">Enabled</option> + <option value="false">Disabled</option> + </param> + <when value="true"> + <param name="metabolomics" type="data" format="tabular" label="Metabolomics data" + help="String specifying the returned metabolite ID format." /> + <param name="metabolome_ids" type="select" label="Metabolite ID format" + help="String specifying the returned metabolite ID format."> + <option value="HMDB">HMDB</option> + <option value="CAS">CAS</option> + <option value="DTXCID">DTXCID</option> + <option value="DTXSID">DTXSID</option> + <option value="SID">SID</option> + <option value="CID">CID</option> + <option value="ChEBI">ChEBI</option> + <option value="KEGG">KEGG</option> + <option value="Drugbank">Drugbank</option> + </param> + </when> + <when value="false"/> + </conditional> + <param name="organism" type="select" label="Supported organisms"> + <option value="hsapiens">Homo sapiens (Human)</option> + <option value="mmusculus">Mus musculus (Mouse)</option> + <option value="rnorvegicus">Rattus Norvegicus (Rat)</option> + <option value="cfamiliaris">Canis lupus familiaris (Dog)</option> + <option value="btaurus">Bos taurus (Cow)</option> + <option value="sscrofa">Sus scrofa (Pig)</option> + <option value="ggallus">Gallus gallus (Chicken)</option> + <option value="xlaevis">Xenopus laevis (Flog)</option> + <option value="drerio">Danio rerio (Zebrafish)</option> + <option value="dmelanogaster">Drosophila melanogaster (Fruit fly)</option> + <option value="celegans">Caenorabditis elegans (Roundworm)</option> + </param> + <param name="databases" type="select" multiple="true" label="Pathway databases" help="Available pathway databases"> + <option value="all" selected="true">All available databases</option> + <option value="kegg">KEGG</option> + <option value="reactome">REACTOME</option> + <option value="wikipathways">WIKIPATHWAYS</option> + <option value="pathbank">PATHBANK</option> + <option value="smpdb">SMPDB (Human only)</option> + <option value="panther">PANTHER (Human only)</option> + <option value="pharmgkb">PHARMGKB (Human only)</option> + </param> + <param name="combine_pvalues" type="select" label="Combine p-values method" help="It specifies the method to combine multiple p-values "> + <option value="stouffer">Stouffer</option> + <option value="fisher">Fisher</option> + <option value="edgington">Edgington</option> + </param> + <param name="padj_method" type="select" label="P-values correction method" help=" Multiple testing corrections adjust + p-values derived from multiple statistical tests to correct for occurrence of false positives"> + <option value="holm">Holm</option> + <option value="hochberg">Hochberg</option> + <option value="hommel">Hommel</option> + <option value="bonferroni">Bonferroni</option> + <option value="BH" selected="true">BH</option> + <option value="BY">BY</option> + </param> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: pathway enrichment"/> + </outputs> + <tests> + <!-- Test only with transcriptomics data --> + <test expect_num_outputs="1"> + <param name="organism" value="hsapiens"/> + <param name="databases" value="kegg"/> + <param name="combine_pvalues" value="stouffer"/> + <param name="padj_method" value="holm"/> + <conditional name="transcriptomics_data"> + <param name="selector" value="true"/> + <param name="transcriptomics" value="transcriptome.tsv"/> + <param name="transcriptome_ids" value="SYMBOL"/> + </conditional> + <output name="output"> + <assert_contents> + <has_size value="43574" delta="300"/> + <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> + </assert_contents> + </output> + </test> + <!-- Test all inputs --> + <test expect_num_outputs="1"> + <param name="organism" value="hsapiens"/> + <param name="databases" value="kegg"/> + <param name="combine_pvalues" value="stouffer"/> + <param name="padj_method" value="holm"/> + <conditional name="transcriptomics_data"> + <param name="selector" value="true"/> + <param name="transcriptomics" value="transcriptome.tsv"/> + <param name="transcriptome_ids" value="SYMBOL"/> + </conditional> + <conditional name="proteomics_data"> + <param name="selector" value="true"/> + <param name="proteomics" value="proteome.tsv"/> + <param name="proteome_ids" value="SYMBOL"/> + </conditional> + <conditional name="metabolomics_data"> + <param name="selector" value="true"/> + <param name="metabolomics" value="metabolome.tsv"/> + <param name="metabolome_ids" value="HMDB"/> + </conditional> + <output name="output"> + <assert_contents> + <has_size value="42541" delta="300"/> + <has_text text="Ubiquinone and other terpenoid-quinone biosynthesis"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +Purpose +======= + +The multiGSEA allows to perform robust GSEA-based pathway enrichment for +multiple omics layers. The enrichment is calculated for each omics layer +separately and aggregated p-values are calculated afterwards to derive a +composite multi-omics pathway enrichment. + +Input requirements +================== + +``multiGSEA`` can be applied with up to three different omics layers. In +principle, the input format is similar between those layers, containing +the feature IDs, the log2 fold change, and the p-Value. + +The columns have to be named as follows: + +:: + + - Symbol (feature ID) + - logFC (log2 fold change) + - pValue + +Two example omics data sets is shown below: + +**Trancriptomics input data** + +================== ========= ============ +Symbol logFC pValue +================== ========= ============ +ENSRNOG00000009450 -3.447792 1.063839e-24 +ENSRNOG00000011858 -2.604610 4.928870e-36 +ENSRNOG00000005438 -2.743588 8.085929e-15 +ENSRNOG00000005697 -3.575947 5.721265e-34 +ENSRNOG00000011130 -2.507097 2.931514e-11 +ENSRNOG00000002265 -2.647413 9.085615e-26 +================== ========= ============ + +**Proteomics input data** + +======== ====== ============ +Symbol logFC pValue +======== ====== ============ +B1WBW4 -4.080 6.027171e-04 +B2RYC9 -2.860 2.937084e-06 +F1LPV8 3.370 2.930764e-13 +F1LR66 5.310 3.580927e-16 +P06685 5.030 1.890405e-18 +P06761 0.324 4.833296e-01 +======== ====== ============ + +Organisms +========= + +``multiGSEA`` can be applied to 11 model organisms: + +- *Homo sapiens* (hsapiens) +- *Mus musculus* (mmusculus) +- *Rattus norvegicus* (rnorvegicus) +- *Canis familiaris* (cfamiliaris) +- *Sus scrofa* (sscrofa) +- *Bos taurus* (btaurus) +- *Danio rerio* (drerio) +- *Gallus gallus* (ggallus) +- *Xaenopus laevis* (xlaevis) +- *Caenorhabditis elegans* (celegans) +- *Drosophila melanogaster* (dmelanogaster) + +Databases +========= + +Depending on the selected organism, several pathway databases can be +queried. + +**H.sapiens** + + - kegg, reactome, wikipathways, panther, pathbank, pharmgkb, smpdb + +**M.musculus, R.norvegicus, B.taurus, C.elegans, D.melanogaster** + + - kegg, reactome, pathbank, wikipathways + +**C.familiaris, S.scrofa, D.rerio, G.gallus** + + - kegg, reactome, wikipathways + +**X.laevis** + + - kegg + +Combining p-values +================== + +multiGSEA provided three different methods to aggregate p-values. These +methods differ in their way how they weight either small or large +p-values. By default, combinePvalues will apply the Z-method or +Stouffer’s method (Stouffer *et al.*, 1949) which has no bias towards +small or large p-values. The widely used Fisher’s combined probability +test (Fisher, 1932) can also be applied but is known for its bias +towards small p-values. Edgington’s method goes the opposite direction +by favoring large p-values (Edgington, 1972). + + +Output format +============= + +The calculated pathway enrichment is sorted based on their combined adjusted p-values. For each individual pathway, the single omics p-Value and adjusted p-Values are collected as well as the combined p-Value and adjusted p-Value. + + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metabolome.tsv Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,4882 @@ +HMDB logFC pValue adj.pValue +HMDB00042 -0.0184063243797361 0.0393850546294737 0.0715518519158232 +HMDB03344 -0.0184063243797361 0.0393850546294737 0.0715518519158232 +HMDB00820 -0.0809343580426596 1.29769217171408e-4 4.58544936100836e-4 +HMDB00863 -0.0809343580426596 1.29769217171408e-4 4.58544936100836e-4 +HMDB06853 -0.0831995371926642 7.40216146766902e-4 0.00215316434714817 +HMDB13785 -0.0831995371926642 7.40216146766902e-4 0.00215316434714817 +HMDB34233 -0.00934945638356588 0.484191596837843 0.563096302375954 +HMDB04296 0.00215711905157612 0.64915129798144 0.715748893346706 +HMDB01167 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14 +HMDB06112 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14 +HMDB31647 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14 +HMDB01106 -0.0347432207851242 0.0326943530012331 0.0615884398787066 +HMDB01888 -0.0347432207851242 0.0326943530012331 0.0615884398787066 +HMDB02134 -0.0347432207851242 0.0326943530012331 0.0615884398787066 +HMDB60177 -0.0347432207851242 0.0326943530012331 0.0615884398787066 +HMDB00119 -0.0937072233758816 4.84523409644223e-5 1.85280300092416e-4 +HMDB00237 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB03052 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB03453 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB06458 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB06961 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB31229 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB31523 -0.0104041409570339 0.208849892788836 0.290116653792384 +HMDB00123 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12 +HMDB14691 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12 +HMDB31239 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12 +HMDB00115 -0.0268586005818108 0.105120388723111 0.163112335693459 +HMDB31608 -0.0268586005818108 0.105120388723111 0.163112335693459 +HMDB13860 -0.00871020591739047 0.00616386659553615 0.0143682826348 +HMDB02039 0.0171869600117898 0.0390684076240339 0.0712300789002475 +HMDB60427 0.0171869600117898 0.0390684076240339 0.0712300789002475 +HMDB00549 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB02523 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB03407 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB10720 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB31209 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB33977 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB34439 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7 +HMDB03609 -0.0414586189510491 6.9920791484094e-9 5.49147139271231e-8 +HMDB39426 -0.0414586189510491 6.9920791484094e-9 5.49147139271231e-8 +HMDB00039 0.022048220035904 0.00188217842601743 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome.tsv Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,8276 @@ +Symbol logFC pValue adj.pValue +IFRD1 2.17100926892448 1.51976984734139e-11 1.257609548675e-7 +FAM129A 1.96701389667949 7.79364076028412e-11 3.22461886456755e-7 +FDFT1 -1.7770896907038 2.49353452977254e-10 6.87799941128926e-7 +ASNS 1.45723078606236 4.70888436048425e-10 9.7415045207518e-7 +CTH 1.57397487228467 1.21773665242265e-9 1.66542814540689e-6 +PCK2 1.38119169411237 1.23327992687474e-9 1.66542814540689e-6 +SPINK6 -1.30950487130349 1.40882139188498e-9 1.66542814540689e-6 +ATF4 3.50982732240442 1.89605895623752e-9 1.79559895382218e-6 +SCARA3 -1.35022041391619 1.95291729116612e-9 1.79559895382218e-6 +PRELID1 1.44681897472319 2.19647632502257e-9 1.81758415895618e-6 +SESN2 1.40215149710929 2.56825592512607e-9 1.93202888912893e-6 +PSAT1 1.22666337268055 2.96854058366878e-9 2.0470561108216e-6 +SLMO2 2.15471474123484 3.57482550112632e-9 2.27551392475541e-6 +CHAC1 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0.964216756731171 0.973774537988059 +AP1S2 -0.00335616310578413 0.964242726800502 0.973774537988059 +CDC42BPB 0.0023782574748239 0.964730727003393 0.974148476626367 +TRIM7 0.00274082585795732 0.96502703822746 0.974328787375822 +TMEM120A 0.00407847598831257 0.965535918530074 0.974723645948074 +SYBU -0.00350040292143117 0.966068644648705 0.975142477978535 +SRSF1 -0.00228015773359225 0.966716136296009 0.97567703718130006 +MBTPS2 -0.00354104380588627 0.967044475107485 0.975889394087127 +C12orf23 -0.00287027664180606 0.967182025636721 0.975909189384693 +CFL1 0.0039210610216064996 0.968050373667712 0.976666281650855 +EXOSC4 -0.00222006729936375 0.968452845420829 0.976953223925072 +PIK3C2B -0.0041849367864879 0.969562454882566 0.977953353748566 +YTHDC1 0.00220885031165086 0.969721086649207 0.977994148936281 +MPP5 -0.00126691663994993 0.97030044524602 0.978459198685208 +FIP1L1_1 -0.0103257158912209 0.97059983132110506 0.978641842839301 +MIEF1 -0.00146377886703242 0.971428634387112 0.979358180988469 +NDEL1 0.00213972947626218 0.971757214720337 0.979521782871646 +MYO1C -0.00166916760927549 0.971827654063591 0.979521782871646 +CASP9 0.00186201421181131 0.972792503342167 0.980374858745151 +CISD1 0.00129134277062803 0.973244279847791 0.980710717942094 +NT5C3A 0.0011852953169722 0.973508123601874 0.98082166127167 +POLR2B 0.00111180683375789 0.973688520027536 0.98082166127167 +ITPRIPL2 0.00273789722934747 0.973771787713174 0.98082166127167 +STRA13 0.00280260282851064 0.973828491723026 0.98082166127167 +EXOC4 -0.00121639189234113 0.97428561420282 0.981162645433654 +HMGN2 0.00438816583687451 0.974689589843927 0.981349602991315 +BUB3 0.00130739815342285 0.974758414039873 0.981349602991315 +POLR3G 0.00467304468681107 0.974827037654213 0.981349602991315 +BCL9 -0.0019075458004103 0.975008122927501 0.981412506656741 +RPL24 -0.00213055857754529 0.975967509165797 0.982249265840489 +SIRT1 0.00172703006692387 0.976076823324029 0.982249265840489 +CENPC -0.00129888560737967 0.976838959527914 0.982896691402418 +PTGS1 0.00283268290649463 0.978988414531366 0.984939711884141 +KDM3A -0.00148481322038485 0.979460667411376 0.985295042891944 +RAB10 0.00128673849019556 0.979867388020873 0.985584372902969 +OS9 -0.00186938532455549 0.98037798441374 0.985870776211496 +SH3PXD2A -0.00203725639538899 0.980390406941921 0.985870776211496 +CRTC3 -0.00150860489831661 0.980790399901103 0.986153166364718 +SRGAP1 0.00141168161596283 0.981644861158653 0.98689238562603 +UCK1 -0.00207958379289508 0.981901194990124 0.987030173535383 +CADM4 0.00177779132718836 0.98230616872059 0.987197539151131 +CKMT1A -8.24257128518191e-4 0.982457662860829 0.987197539151131 +HEXA 8.28900607565686e-4 0.982475711945914 0.987197539151131 +KLHDC10 -0.00341741615570612 0.982544886096521 0.987197539151131 +HIP1R -9.96352489925911e-4 0.982833167881795 0.987301892689877 +VBP1 -0.00102813244280853 0.982887370631929 0.987301892689877 +PLCL2 -0.00197352140785245 0.983300754292166 0.987597249880771 +ANXA6 -9.63957809009486e-4 0.983750862718863 0.987929416140606 +ACTR1A -0.00142398778348962 0.983992468872903 0.988052139294172 +SIRPA -0.0011483141202166501 0.984319531238841 0.988260631036327 +CEP85L 0.0011241719714441 0.984618757147316 0.988441127671241 +GEMIN4 8.85391638851374e-4 0.985282861225476 0.988987830742457 +TRAPPC6B 0.00127697257047288 0.985429266561242 0.989014818774321 +C1orf198 0.00181331241736693 0.985800026473636 0.989266943859973 +FAM188B -0.00290305790297918 0.986842246699505 0.990192747840234 +KAL1 -0.00468633242773997 0.98701951895038 0.990250547928516 +MIER3 0.00298353305365939 0.987369056492619 0.990312922998574 +HN1 -0.00142430503294744 0.987412980075915 0.990312922998574 +HSPB8 7.76206291130954e-4 0.987440716333684 0.990312922998574 +SRP14 0.0010232057036319 0.987681326555633 0.990434195013071 +PRPS1 -6.45398851954582e-4 0.988580959526359 0.991216217142932 +CSNK2B 4.81976873256684e-4 0.989123670891745 0.991640220090767 +USP32 -5.08633248005097e-4 0.98958692310659 0.991984468650155 +GEMIN7 -0.00125412327971297 0.989962197266786 0.992240453292473 +RIPK2 -6.27242303687048e-4 0.990514276757734 0.992673566691322 +SLC9A6 -7.59651130186612e-4 0.990767405389334 0.992807008912174 +GUSB -7.2436835249956e-4 0.991577578344927 0.993498542293773 +SEH1L 5.4658008260855e-4 0.991948490806523 0.993749850051329 +PWWP2B 0.00121275638794849 0.992627852111002 0.994310068541162 +AP5B1 -4.32669290459486e-4 0.993432924620357 0.994996060425255 +ARNTL 3.16052536415867e-4 0.993732102100046 0.995115782519309 +THAP11 0.00103464439352674 0.99379296999874 0.995115782519309 +REXO1 0.00125420672958132 0.994464514478296 0.995667738331264 +TTC21A -7.81532977215171e-4 0.995387384769103 0.996471160048914 +TPM3 -4.02905617320926e-4 0.995744658186035 0.996630443760696 +PPP1R13B 5.1600456486689e-4 0.995787372690445 0.996630443760696 +MICAL2 2.76393643596329e-4 0.995997543876262 0.996720241332213 +FN1 -2.58494133370313e-4 0.99689891635036 0.997434357481888 +ZBTB5 -1.37914580930598e-4 0.996952213985824 0.997434357481888 +COPA 1.05578131729622e-4 0.998444512763599 0.998806617881865 +AKTIP 1.50880700191536e-4 0.999454954517943 0.999696573025018 +XRCC1 -1.2372981342601e-5 0.999772026690978 0.999859015825647 +SUPT4H1 -3.05334106771582e-5 0.999859015825647 0.999859015825647
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome.tsv Wed Jun 07 19:48:50 2023 +0000 @@ -0,0 +1,15175 @@ +Symbol logFC pValue adj.pValue +STC2 0.704500282226347 3.71089306872736e-14 5.63090914248689e-10 +ASNS 0.627966319665099 2.0255326292911e-13 1.53677160584316e-9 +PCK2 0.619355311651102 7.77477603404156e-13 3.93248171801822e-9 +FAM129A 0.880826438814874 1.06943563433091e-12 4.05690407883431e-9 +NUPR1 0.588841194242637 1.54636710326692e-12 4.69291488499446e-9 +ASS1 0.624138659380686 2.41695823247016e-12 6.11248736991704e-9 +TRIB3 0.86297487467659 3.46130939111073e-12 7.50312981438775e-9 +PSAT1 0.469619454647728 1.41593552178526e-11 2.68567570094618e-8 +FADS2 -0.397872623139451 2.00851788591982e-11 3.38636115566082e-8 +BMF -0.590480389664462 3.8446423466847e-11 5.83386029685936e-8 +SESN2 0.609514732887674 4.78507080806277e-11 6.60078767650405e-8 +GDF15 0.936936029787823 5.45997234968492e-11 6.90413503617659e-8 +WARS 0.335627820987674 7.4570266737941e-11 8.70407098062705e-8 +SLC6A9 0.406200205524983 1.12457110729216e-10 1.21887442728937e-7 +CHAC1 1.45474233419102 1.46636951721807e-10 1.4833794036178e-7 +VEGFA 0.381554890128001 1.8661105799545e-10 1.72246954436364e-7 +GPT2 0.515468087344662 1.92974708410319e-10 1.72246954436364e-7 +MARS 0.309316030617479 2.2575158143115e-10 1.90308583146459e-7 +CARS 0.375811955851783 2.74959554544042e-10 2.11962735044355e-7 +MTHFD2 0.468336628805509 2.79376215954072e-10 2.11962735044355e-7 +INSIG1 -0.508872341985173 3.51468457261962e-10 2.53961065261572e-7 +LARP6 0.651200265452626 3.9000696993804e-10 2.57390487303515e-7 +EIF4EBP1 0.39781539983742 3.90139792275e-10 2.57390487303515e-7 +SARS 0.28266275512208 4.92761973719958e-10 3.09233070885333e-7 +IDH1 0.291986761085429 5.09478500865515e-10 3.09233070885333e-7 +CEBPG 0.425667840930084 5.66385614668879e-10 3.30551358345599e-7 +PSPH 0.435623588643199 5.92600427114492e-10 3.33041440038345e-7 +ASF1B -0.362870511536212 6.394431595813e-10 3.46532517981666e-7 +UNC5B 1.6816745643023 7.72770722162363e-10 4.04345618554886e-7 +AJUBA 0.443379616186069 8.75626472578165e-10 4.42891869830036e-7 +GARS 0.324448707903362 1.00110053900395e-9 4.90022567059547e-7 +SLC1A5 0.257571321924166 1.31058087788177e-9 6.06702929384363e-7 +C6orf48 0.349759534720501 1.31944092985923e-9 6.06702929384363e-7 +BCAT1 0.457197936829043 1.84698044952342e-9 8.24296510031423e-7 +AMIGO2 0.416562600697803 2.37222347980217e-9 1.00004628327156e-6 +CDKN2C -0.282700228263487 2.37258904690762e-9 1.00004628327156e-6 +ATF3 0.671925395165331 2.50411962501266e-9 1.02695976189033e-6 +MEOX1 -0.68834135622312 2.80771464561384e-9 1.10557404664781e-6 +CTH 0.869872912460933 2.84153076441706e-9 1.10557404664781e-6 +ALDH1L2 0.7713556268181 3.4046575828848e-9 1.29155685406735e-6 +S100P 1.12974082445842 3.97201032560321e-9 1.47003133367569e-6 +FDFT1 -0.294031210384657 4.8822183870755e-9 1.76387575727342e-6 +KRT19 -0.424151176401533 6.42997143542185e-9 2.26903224560677e-6 +IARS 0.20763052159502501 7.69697064653723e-9 2.63303671383474e-6 +IL20RB 0.733295193003586 7.80853117981833e-9 2.63303671383474e-6 +SCD -0.217792840011739 8.19842770455638e-9 2.70441178236823e-6 +IGSF10 -0.20716826969625 9.46637151933383e-9 3.05622811562493e-6 +GADD45A 0.539934056770522 1.06221034982652e-8 3.35791246838907e-6 +XPOT 0.268979736455839 1.13306810802815e-8 3.50881132065698e-6 +AARS 0.222853251872265 1.19344915903575e-8 3.58463419823735e-6 +YARS 0.215534347928307 1.20479994800386e-8 3.58463419823735e-6 +ERRFI1 0.421169493373689 1.24880776104427e-8 3.64411710886264e-6 +RRM2 -0.317872011771425 1.50347425878583e-8 4.28813234604051e-6 +IDI1 -0.411509181300695 1.52602574592189e-8 4.28813234604051e-6 +ASS1P9 1.15397931088342 1.58030820588866e-8 4.35992667566447e-6 +VLDLR 0.672932216314967 1.6698977162507e-8 4.45630020021719e-6 +CLGN 0.404117751484052 1.69384994276749e-8 4.45630020021719e-6 +RGCC -0.453512271811646 1.71237430572711e-8 4.45630020021719e-6 +SHMT2 0.235611237430561 1.74124966656655e-8 4.45630020021719e-6 +PLCXD3 -0.463524617673655 1.7620799526363e-8 4.45630020021719e-6 +GAS5 0.247672757375438 1.89946395806483e-8 4.7249944425698e-6 +LGR4 -0.28645249491221 1.93757021218831e-8 4.74014607937185e-6 +SLC1A4 0.267633805381842 1.96803218004763e-8 4.74014607937185e-6 +LONP1 0.241835246978595 2.01391964713265e-8 4.77487761337357e-6 +S100A4 -0.237850711251943 2.14786253473932e-8 5.01410247725145e-6 +PHGDH 0.229947526233384 2.28739361874053e-8 5.25892587435891e-6 +MAP1A -0.521181751998103 2.33716899660934e-8 5.27915478291686e-6 +RP11-382M14.1 1.27658128760577 2.3955760049532e-8 5.27915478291686e-6 +ADM2 1.25497133135791 2.40056465019944e-8 5.27915478291686e-6 +ASS1P12 1.13275095205903 2.58397198936279e-8 5.60131299522728e-6 +TUBA1A -0.280369608550124 2.64766461233519e-8 5.65854406022171e-6 +TIMP4 0.583418059325131 2.74791377565825e-8 5.70382329043418e-6 +PPP1R15A 0.572422339238252 2.77757100929054e-8 5.70382329043418e-6 +PRKCB -0.478369037935187 2.78161937190015e-8 5.70382329043418e-6 +PSAT1P3 0.794660352923572 2.9611166569063e-8 5.99093122025282e-6 +ATF4 0.183973975082908 3.08966416300889e-8 6.09735620013072e-6 +ASS1P11 1.22103280295456 3.13231732937496e-8 6.09735620013072e-6 +DDIT3 0.857426072047891 3.14055342485103e-8 6.09735620013072e-6 +TCEA1P2 0.402829917319312 3.1747634257474e-8 6.09735620013072e-6 +KCTD15 0.270888100570315 3.21463355746973e-8 6.09735620013072e-6 +SLC7A11 0.274013428607222 3.37505130599036e-8 6.32259611322195e-6 +ETV5 1.24125642334775 3.74728252919992e-8 6.93430062171703e-6 +DHCR24 -0.196394384351996 4.28396294245522e-8 7.83191008298982e-6 +AKAP12 -0.241504185052597 4.34385031337442e-8 7.84685531608851e-6 +CBS 0.223518971310903 4.54626083419868e-8 8.11587787036832e-6 +FADS1 -0.181398069631374 4.67186760315064e-8 8.24313011746602e-6 +PALMD -0.335422179715229 4.8430947785682e-8 8.44702530689585e-6 +METTL7A -0.660763679550601 5.00416257329574e-8 8.6287685099079e-6 +UHRF1BP1 0.301784045643583 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