Merge pull request #141 from bcbio/devel

bump to 0.4.4

Author: lpantano

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.4.3
+Version: 0.4.4
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.

NEWS.md

@@ -1,3 +1,33 @@
+# bcbioR 0.4.4
+
+init QC single cell adding init file for params for single QC #123
+on disk seurat object How to make a Seurat object with BPcells-good for big objects #128
+add gene name to count matrix Add gene name to counts files rnaseq-reports#8
+Add style checks to rnaseq and singlecell repositories
+Restructure singlecell readmes
+
+# bcbioR 0.4.3
+
+migrate rnaseq templates to its own repo #120
+add HD visium QC #101
+add HD visum clustering #102
+include code to generate files for DEGpattern #116
+double code for single cell #130
+adapt to QC to ATACseq #133
+fix error in names #132
+fix GSEA rnaseq error and styling code bcbio/rnaseq-reports#2
+
+# bcbioR 0.4.2
+
+Filter genes according biotype or gene name #117
+Add Visium HD QC #101 #115
+Add degPattern template #97
+Collapse multiple params files #65
+Add rmaseq library links #60
+Fix version comparison #104
+Save log object in sc data #105
+More docs for clusters ids #106
+
 # bcbioR 0.4.1
 
 - in DEG.Rmd, write expression table only once	https://github.com/bcbio/bcbioR/issues/63

R/helpers.R

@@ -212,11 +212,11 @@ copy_templates <- function(path, pipeline, org=NULL){
     names(repos)="rnaseq-reports"
   }else if(pipeline=="singlecell"){
     parts = c("templates/singlecell")
-    # repos = "https://github.com/bcbio/singlecell-reports"
-    # names(repos)="singlecell-reports"
+    repos = "https://github.com/bcbio/singlecell-reports/archive/refs/heads/main.zip"
+    names(repos)="singlecell-reports"
     apps=c(apps, scRNAseq_qc="https://github.com/hbc/scRNAseq_qc_app/archive/refs/heads/main.zip")
-  }else if(pipeline=="singlecell_delux"){
-    parts = c("templates/singlecell_delux")
+  # }else if(pipeline=="singlecell_delux"){
+  #   parts = c("templates/singlecell_delux")
   }else if(pipeline=="multiomics"){
     parts = c("templates/multiomics")
   }else if(pipeline=="spatial"){

README.md

@@ -43,28 +43,29 @@ bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")
 
 ## Supported analyses
 
-- base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
-- [rnaseq-reports](https://github.com/bcbio/rnaseq-reports):
-  - 01_quality_assessment/QC.Rmd: ![](https://img.shields.io/badge/status-stable-green)
-  - 02_differential_expression/DEG.Rmd: ![](https://img.shields.io/badge/status-stable-green)
-  - 03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 03_functional/GSVA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 03_functional/Immune-deconvolution.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 03_comparative/Pair-wise-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 03_comparative/Intersections.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 04_gene_patterns/WGCNA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-  - 05_gene_patterns/DEGpattern.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
-- [singlecell/01_quality_assessment/scRNA_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-stable-green)
-- [singlecell/01_quality_assessment/scATAC_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
-- [singlecell/02_differential_expression/scRNA_MAST.Rmd](singlecell/02_differential_expression/scRNA_MAST.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [singlecell/02_differential_expression/scRNA_pseudobulk.Rmd](singlecell/02_differential_expression/scRNA_pseudobulk.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [singlecell/04_compositional/propeller.Rmd](singlecell/04_compositional/propeller.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
-- [singlecell/04_compositional/sccomp.Rmd](singlecell/04_compositional/sccomp.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
-- [singlecell_delux/01_CellToCell/cellchat.Rmd](singlecell_delux/01_CellToCell/cellchat.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
-- [chipseq/02_diffbind/diffbind.Rmd](chipseq/02_diffbind/diffbind.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [chipseq/01_quality_assessment/QC.Rmd](chipseq/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [spatial/visium/01_quality_assessment/qc.Rmd](spatial/visium/01_quality_assessment/qc.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
-- [spatial/cosmx/01_quality_assessment/QC.Rmd](spatial/cosmx/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
+-   base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+-   [rnaseq-reports](https://github.com/bcbio/rnaseq-reports):
+    -   01_quality_assessment/QC.Rmd ![](https://img.shields.io/badge/status-stable-green)
+    -   02_differential_expression/DEG.Rmd ![](https://img.shields.io/badge/status-stable-green)
+    -   03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   03_functional/GSVA.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   03_functional/Immune-deconvolution.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   03_comparative/Pair-wise-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   03_comparative/Intersections.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   04_gene_patterns/WGCNA.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   05_gene_patterns/DEGpattern.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+-   [single-cell](https://github.com/bcbio/rnaseq-reports)
+    -   singlecell/01_quality_assessment/scRNA_QC.Rmd
+    -   01_quality_assessment/scATAC_QC.Rmd ![](https://img.shields.io/badge/status-draft-grey)
+    -   02_differential_expression/scRNA_MAST.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   02_differential_expression/scRNA_pseudobulk.Rmd ![](https://img.shields.io/badge/status-alpha-yellow)
+    -   singlecell/04_compositional/propeller.Rmd ![](https://img.shields.io/badge/status-draft-grey)
+    -   04_compositional/sccomp.Rmd ![](https://img.shields.io/badge/status-draft-grey)
+    -   05_signaling/cellchat.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
+-   [chipseq/02_diffbind/diffbind.Rmd](inst/templates/chipseq/02_diffbind/diffbind.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
+-   [chipseq/01_quality_assessment/QC.Rmd](inst/templates/chipseq/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
+-   [spatial/visium/01_quality_assessment/qc.Rmd](inst/templates/spatial/visium/01_quality_assessment/qc.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
+-   [spatial/cosmx/01_quality_assessment/QC.Rmd](inst/templates/spatial/cosmx/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
 
 ### Discover more…