Merge branch 'scrnaseq-patch'

Author: u8sand

appyters/scRNA_seq/appyter.json

@@ -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": [

appyters/scRNA_seq/setup.R

@@ -1,3 +1,5 @@
+install.packages("R.utils")
+install.packages("RCurl")
 install.packages("dplyr")
 install.packages("tibble")
 install.packages("Matrix")
@@ -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")
 

appyters/scRNA_seq/utils.py

@@ -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: