# HG changeset patch
# User iuc
# Date 1726317775 0
# Node ID 5dada6f760470bd40c74d0929397f472412e42a7
# Parent 9f354c7c8c921bef1afc2913abc839b4ac61958e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
diff -r 9f354c7c8c92 -r 5dada6f76047 README.md
--- a/README.md Tue Aug 20 09:52:24 2024 +0000
+++ b/README.md Sat Sep 14 12:42:55 2024 +0000
@@ -25,6 +25,7 @@
`pp.highly_variable_genes` | Extract highly variable genes
`pp.subsample` | Subsample to a fraction of the number of observations
`pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts
+ `pp.scrublet` | Predict doublets
3. Normalize (`normalize.xml`)
@@ -34,14 +35,18 @@
`pp.recipe_zheng17` | Normalization and filtering as of [Zheng17]
`pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17]
`pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15]
+ `external.pp.magic` | Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API
4. Remove confounders (`remove_confounder.xml`)
Methods | Description
--- | ---
`pp.regress_out` | Regress out unwanted sources of variation
- `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors
+
`pp.combat` | ComBat function for batch effect correction
+ `external.pp.bbknn` | Batch effect removal with Batch balanced KNN (BBKNN)
+ `external.pp.harmony_integrate` | Integrate multiple single-cell experiments with Harmony
+ `external.pp.scanorama_integrate` | Integrate multiple single-cell experiments with Scanorama
5. Clustering, embedding and trajectory inference (`cluster_reduce_dimension.xml`)
@@ -49,14 +54,14 @@
--- | ---
`tl.louvain` | Cluster cells into subgroups
`tl.leiden` | Cluster cells into subgroups
- `tl.pca` | Principal component analysis
- `pp.pca` | Principal component analysis (appears to be the same func...)
+ `pp.pca` | Principal component analysis
`tl.diffmap` | Diffusion Maps
`tl.tsne` | t-SNE
`tl.umap` | Embed the neighborhood graph using UMAP
`tl.draw_graph` | Force-directed graph drawing
`tl.dpt` | Infer progression of cells through geodesic distance along the graph
`tl.paga` | Mapping out the coarse-grained connectivity structures of complex manifolds
+ `tl.embedding_density` | Calculate the density of cells in an embedding (per condition)
6. Plot (`plot.xml`)
@@ -66,18 +71,20 @@
--- | ---
`pl.scatter` | Scatter plot along observations or variables axes
`pl.heatmap` | Heatmap of the expression values of set of genes
+ `pl.tracksplot` | Tracks plot of the expression values per cell
`pl.dotplot` | Makes a dot plot of the expression values
`pl.violin` | Violin plot
`pl.stacked_violin` | Stacked violin plots
`pl.matrixplot` | Heatmap of the mean expression values per cluster
`pl.clustermap` | Hierarchically-clustered heatmap
-
+
2. Preprocessing
Methods | Description
--- | ---
`pl.highest_expr_genes` | Plot the fraction of counts assigned to each gene over all cells
`pl.highly_variable_genes` | Plot dispersions versus means for genes
+ `pl.scrublet_score_distribution` | Histogram of doublet scores
3. PCA
@@ -96,12 +103,13 @@
`pl.umap` | Scatter plot in UMAP basis
`pl.diffmap` | Scatter plot in Diffusion Map basis
`pl.draw_graph` | Scatter plot in graph-drawing basis
+ `pl.embedding_density` | Density of cells in an embedding (per condition)
5. Branching trajectories and pseudotime, clustering
Methods | Description
--- | ---
- `pl.dpt_groups_pseudotime` | Plot groups and pseudotime
+
`pl.dpt_timeseries` | Heatmap of pseudotime series
`pl.paga` | Plot the abstracted graph through thresholding low-connectivity edges
`pl.paga_compare` | Scatter and PAGA graph side-by-side
@@ -113,3 +121,8 @@
--- | ---
`pl.rank_genes_groups` | Plot ranking of genes using dotplot plot
`pl.rank_genes_groups_violin` | Plot ranking of genes for all tested comparisons
+ `pl.rank_genes_groups_stacked_violin` | Plot ranking of genes as stacked violin plot
+ `pl.rank_genes_groups_heatmap` | Plot ranking of genes as heatmap plot
+ `pl.rank_genes_groups_dotplot` | Plot ranking of genes as dotplot plot
+ `pl.rank_genes_groups_matrixplot` | Plot ranking of genes as matrixplot plot
+ `pl.rank_genes_groups_tracksplot` | Plot ranking of genes as tracksplot plot
diff -r 9f354c7c8c92 -r 5dada6f76047 macros.xml
--- a/macros.xml Tue Aug 20 09:52:24 2024 +0000
+++ b/macros.xml Sat Sep 14 12:42:55 2024 +0000
@@ -1,17 +1,15 @@
- 1.9.6
- 4
- 21.09
+ 1.10.2
+ 0
+ 21.09
scanpy
- loompy
- leidenalg
- louvain
- pandas
- matplotlib
- seaborn
- magic-impute
+ anndata
+ numpy
+ pandas
+ scipy
+ statsmodels
@@ -22,7 +20,7 @@
-
+
@@ -31,28 +29,13 @@
10.1093/gigascience/giaa102
-
-
-
- '$hidden_output' &&
-python '$script_file' >> '$hidden_output' &&
-ls . >> '$hidden_output' &&
-touch 'anndata_info.txt' &&
-cat 'anndata_info.txt' @CMD_prettify_stdout@
- ]]>
-
-
-
+
+
+
-
+
@@ -62,58 +45,55 @@
-
+
-
-
-
-
+
+
+
+
advanced_common['show_log']
+
+
+
+
+
-
-
-
-
+
+
+
-
+
-
+
+
-
@@ -393,141 +373,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 0:
- #set $var_group_positions=[]
- #set $var_group_labels=[]
- #for $i, $s in enumerate($method.var_group_positions)
- #silent $var_group_positions.append((int($s.start), int($s.end)))
- #silent $var_group_labels.append(str($s.label))
- #end for
- var_group_positions=$var_group_positions,
- var_group_labels=$var_group_labels,
- #end if
- #if str($method.var_group_rotation) != ''
- var_group_rotation=$method.var_group_rotation,
- #end if
- #if $method.figsize.test == 'yes'
- figsize=($method.figsize.width, $method.figsize.height),
- #end if
- #if $method.layer
- layer='$method.layer',
- #end if
- ]]>
@@ -679,500 +524,298 @@
-
+
-
-
-
-
-
-
-
-
-
-
-
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+ density_norm='$method.violin_plot.density_norm',
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
- 0
- #set $components=[]
- #for $i, $s in enumerate($method.plot.components)
- #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
- #end for
- components=$components,
-#end if
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
-
-
-
-
+
+
+
+
-
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
+
+
+
+
+
+
+
-
-
-
-
+
+
+
+
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
- 0:
+ #set $var_group_positions=[]
+ #set $var_group_labels=[]
+ #for $i, $s in enumerate($method.var_group_positions)
+ #silent $var_group_positions.append((int($s.start), int($s.end)))
+ #silent $var_group_labels.append(str($s.label))
+ #end for
+ var_group_positions=$var_group_positions,
+ var_group_labels=$var_group_labels,
#end if
- #if str($method.dot_max) != ''
- dot_max=$method.dot_max,
+ #if str($method.var_group_rotation) != '':
+ var_group_rotation=$method.var_group_rotation,
#end if
- #if str($method.dot_min) != ''
- dot_min=$method.dot_min,
- #end if
- @CMD_params_matplotlib_pyplot_scatter@
+ @CMD_PARAMS_FIGSIZE@
+ @CMD_PARAM_LAYER@
]]>
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
-
-
+
+
@@ -1194,106 +837,627 @@
-
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0:
+ #set $components=[]
+ #for $i, $s in enumerate($method.plot.components)
+ #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
+ #end for
+ components=$components,
+#end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 9f354c7c8c92 -r 5dada6f76047 normalize.xml
--- a/normalize.xml Tue Aug 20 09:52:24 2024 +0000
+++ b/normalize.xml Sat Sep 14 12:42:55 2024 +0000
@@ -1,45 +1,40 @@
-
- and impute with scanpy
+
+ and impute
macros.xml
-
+
+ magic-impute
+
+@CMD_ANNDATA_WRITE_OUTPUTS@
+ ]]>
+
@@ -108,63 +113,50 @@
+
-
-
+
-
-
+
+
-
-
-
-
-
-
-
+
+
-
-
+
+
-
-
-
-
-
-
+
-
+
-
+
-
-
-
-
+
+
+
+
+ help="For extremely large datasets, using n_pca less than 20 allows neighborhoods to be calculated in roughly log(n_samples) time. If not set, no PCA is performed."/>
-
+
-
+
@@ -173,41 +165,39 @@
+
+
-
-
+
-
-
-
-
-
-
+
+
+
-
-
-
-
+
+
+
-
-
+
-
-
-
-
-
-
-
+
+
+
-
-
+
-
-
+
-
+
+
+
-
-
+
-
-
+
+
+
-
-
+
@@ -296,7 +304,7 @@
-
+
`__
+`__
Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
@@ -369,7 +380,7 @@
MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold.
-The algorithm implemented here has changed primarily in two ways compared to the algorithm described in Van Dijk D et al. (2018).
+The algorithm implemented here has changed primarily in two ways compared to the algorithm described in Van Dijk D et al. (2018).
- Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability.
- Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements.
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad
Binary file test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/external.pp.bbknn.krumsiek11.h5ad
Binary file test-data/external.pp.bbknn.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/external.pp.magic.all_genes.krumsiek11.h5ad
Binary file test-data/external.pp.magic.all_genes.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/external.pp.magic.pca_only.krumsiek11.h5ad
Binary file test-data/external.pp.magic.pca_only.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pbmc68k_reduced.h5ad
Binary file test-data/pbmc68k_reduced.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.clustermap.krumsiek11.png
Binary file test-data/pl.clustermap.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png
Binary file test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.dotplot.krumsiek11.png
Binary file test-data/pl.dotplot.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png
Binary file test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.draw_graph.png
Binary file test-data/pl.draw_graph.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.embedding_density.pbmc68k_reduced.png
Binary file test-data/pl.embedding_density.pbmc68k_reduced.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.heatmap.krumsiek11.png
Binary file test-data/pl.heatmap.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png
Binary file test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.highly_variable_genes.seurat.blobs.png
Binary file test-data/pl.highly_variable_genes.seurat.blobs.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.matrixplot.krumsiek11.png
Binary file test-data/pl.matrixplot.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.paga.paul15_gauss_braycurtis.png
Binary file test-data/pl.paga.paul15_gauss_braycurtis.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.paga_compare.paul15_gauss_braycurtis.png
Binary file test-data/pl.paga_compare.paul15_gauss_braycurtis.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf
Binary file test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.pca_loadings.pp.pca.krumsiek11.png
Binary file test-data/pl.pca_loadings.pp.pca.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.pca_overview.pp.pca.krumsiek11.png
Binary file test-data/pl.pca_overview.pp.pca.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png
Binary file test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png
Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png
Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png
Binary file test-data/pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_violin.Ery.png
Binary file test-data/pl.rank_genes_groups_violin.Ery.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_violin.Mk.png
Binary file test-data/pl.rank_genes_groups_violin.Mk.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_violin.Mo.png
Binary file test-data/pl.rank_genes_groups_violin.Mo.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_violin.Neu.png
Binary file test-data/pl.rank_genes_groups_violin.Neu.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.rank_genes_groups_violin.progenitor.png
Binary file test-data/pl.rank_genes_groups_violin.progenitor.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.scatter.krumsiek11.png
Binary file test-data/pl.scatter.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.scatter.pbmc68k_reduced.png
Binary file test-data/pl.scatter.pbmc68k_reduced.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.scatter.umap.pbmc68k_reduced.png
Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.scrublet_score_distribution.png
Binary file test-data/pl.scrublet_score_distribution.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.stacked_violin.krumsiek11.png
Binary file test-data/pl.stacked_violin.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png
Binary file test-data/pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.tsne.krumsiek11.png
Binary file test-data/pl.tsne.krumsiek11.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png
Binary file test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pl.violin.pbmc68k_reduced_custom.png
Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad
Binary file test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.downsample_counts.random-randint.h5ad
Binary file test-data/pp.downsample_counts.random-randint.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.filter_cells.krumsiek11-max_genes.h5ad
Binary file test-data/pp.filter_cells.krumsiek11-max_genes.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.filter_cells.krumsiek11-min_counts.h5ad
Binary file test-data/pp.filter_cells.krumsiek11-min_counts.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.filter_genes.krumsiek11-min_counts.h5ad
Binary file test-data/pp.filter_genes.krumsiek11-min_counts.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.filter_rank_genes_groups.h5ad
Binary file test-data/pp.filter_rank_genes_groups.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad
Binary file test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.log1p.krumsiek11.h5ad
Binary file test-data/pp.log1p.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.normalize_total.krumsiek11.h5ad
Binary file test-data/pp.normalize_total.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.pca.krumsiek11.batch.h5ad
Binary file test-data/pp.pca.krumsiek11.batch.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.pca.krumsiek11_chunk.h5ad
Binary file test-data/pp.pca.krumsiek11_chunk.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.recipe_seurat.recipe_zheng17.h5ad
Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad
Binary file test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.recipe_zheng17.random-randint.h5ad
Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.scale.krumsiek11.h5ad
Binary file test-data/pp.scale.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.scale_max_value.krumsiek11.h5ad
Binary file test-data/pp.scale_max_value.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.scrublet.krumsiek11.h5ad
Binary file test-data/pp.scrublet.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.sqrt.krumsiek11.h5ad
Binary file test-data/pp.sqrt.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.subsample.krumsiek11_fraction.h5ad
Binary file test-data/pp.subsample.krumsiek11_fraction.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/pp.subsample.krumsiek11_n_obs.h5ad
Binary file test-data/pp.subsample.krumsiek11_n_obs.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/random-randint.h5ad
Binary file test-data/random-randint.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/sparce_csr_matrix.h5ad
Binary file test-data/sparce_csr_matrix.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad
Binary file test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad
Binary file test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad
Binary file test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.score_genes.krumsiek11.h5ad
Binary file test-data/tl.score_genes.krumsiek11.h5ad has changed
diff -r 9f354c7c8c92 -r 5dada6f76047 test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad
Binary file test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad has changed