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[scRNA_seq]: Skip rug plots for missing cell type libraries #902

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u8sand wants to merge 4 commits into from
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[scRNA_seq]: Skip rug plots for missing cell type libraries #902

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50593e6
[scRNA_seq]: Skip rug plots for missing cell type libraries
u8sand Jul 3, 2024
3ce6e82
[scRNA_seq]: Fixes #836 (hopefully)
u8sand Jul 3, 2024
1f533f9
Merge branch 'main' into scrnaseq-patch
u8sand Sep 15, 2025
3255e5c
[scRNA_seq]: 0.2.8
u8sand Sep 15, 2025
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2 changes: 1 addition & 1 deletion appyters/scRNA_seq/appyter.json
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Expand Up @@ -2,7 +2,7 @@
"$schema": "https://raw.githubusercontent.com/MaayanLab/appyter-catalog/main/schema/appyter-validator.json",
"name": "scRNA_seq",
"title": "Single cell RNA-seq analysis pipeline",
"version": "0.2.7",
"version": "0.2.8",
"description": "scRNA-seq analysis pipeline enables users to analyze and visualize scRNA-seq datasets with state-of-the-art algorithms and visualization methods.",
"image": "screenshot.png",
"authors": [
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4 changes: 3 additions & 1 deletion appyters/scRNA_seq/setup.R
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@@ -1,3 +1,5 @@
install.packages("R.utils")
install.packages("RCurl")
install.packages("dplyr")
install.packages("tibble")
install.packages("Matrix")
Expand All @@ -10,9 +12,9 @@ install.packages("statmod")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("DESeq2")
BiocManager::install("limma")
BiocManager::install("edgeR")
BiocManager::install("DESeq2")

install.packages("https://cran.r-project.org/src/contrib/Archive/XML/XML_3.98-1.20.tar.gz")

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1 change: 1 addition & 0 deletions appyters/scRNA_seq/utils.py
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Expand Up @@ -1170,6 +1170,7 @@ def plot_protrack(libraries, tmp_adata, bool_plot_rug=True, bool_plot_dendrogram
adata_heatmap.obs = adata_heatmap.obs.T.drop_duplicates().T
new_library_filename = extract_library_name(library_filename)
library_name = library_filename+"_0"
if library_name not in adata_heatmap.obs.columns: continue
clean_library_filename = {library_name: new_library_filename}
new_cols = list()
for col in adata_heatmap.obs.columns:
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