From 50593e61355fa41a201ab8f415021ed2fbe2d7e7 Mon Sep 17 00:00:00 2001 From: "Daniel J. B. Clarke" Date: Wed, 3 Jul 2024 16:26:31 -0400 Subject: [PATCH 1/3] [scRNA_seq]: Skip rug plots for missing cell type libraries --- appyters/scRNA_seq/appyter.json | 2 +- appyters/scRNA_seq/utils.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/appyters/scRNA_seq/appyter.json b/appyters/scRNA_seq/appyter.json index f1af43d15..6bbcdbbff 100644 --- a/appyters/scRNA_seq/appyter.json +++ b/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": "0.2.6", + "version": "0.2.7", "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": [ diff --git a/appyters/scRNA_seq/utils.py b/appyters/scRNA_seq/utils.py index fa5fee38a..4c90f16b4 100644 --- a/appyters/scRNA_seq/utils.py +++ b/appyters/scRNA_seq/utils.py @@ -1134,6 +1134,7 @@ 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: From 3ce6e82f8911642127c10b78d9a4da27cb9cdc75 Mon Sep 17 00:00:00 2001 From: "Daniel J. B. Clarke" Date: Wed, 3 Jul 2024 16:29:26 -0400 Subject: [PATCH 2/3] [scRNA_seq]: Fixes #836 (hopefully) --- appyters/scRNA_seq/setup.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/appyters/scRNA_seq/setup.R b/appyters/scRNA_seq/setup.R index 229103fa7..1e4a5cfa6 100644 --- a/appyters/scRNA_seq/setup.R +++ b/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") From 3255e5ca06b3f8cc17564d314c44d2688916e03a Mon Sep 17 00:00:00 2001 From: Daniel Clarke Date: Mon, 15 Sep 2025 12:26:41 -0400 Subject: [PATCH 3/3] [scRNA_seq]: 0.2.8 --- appyters/scRNA_seq/appyter.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/appyters/scRNA_seq/appyter.json b/appyters/scRNA_seq/appyter.json index 6bbcdbbff..cf771c4df 100644 --- a/appyters/scRNA_seq/appyter.json +++ b/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": [