bcbioR 0.4.1

in DEG.Rmd, write expression table only once #63
add methods to RNA QC and DE templates #61
sc DE pseudobulk
sc DE MAST
compositional analysis scRNA
entrezid for enrichment analysesS v0.4.1 P1
subset data based on metadata file. #64
ATACseq QC report
Add WGCNA analysis to RNAseq
bug, should be !is.na #73
line of code in volcano plot causes odd figures #70
volcano plot colors #74
remove inline option in RMD #78
change x lab to reads #75
Visium RMD template
fix mouse genome for nfcore and templates
adapt to mouse and another genome in the DE RNAseq template #80
Change to Annotation Hub #94

bcbioR 0.3.1

Fix bugs in RNAseq
Add function to set up library

bcbioR 0.3.0

re-structure templates
Add text with best practices
Reproducibility:
- test data for RNAseq, singlecell, CHIPseq
Base project:
- Guidelines to create repo easily
- Example Rmd with headers and aesthetics
RNASEQ
- Use provenance for FA in DE report
- Support multiple comparisons
New templates:
- methylation - draft
- singcell cell QC and Inegration - stable
- scQC shiny app - stable
- chipseq QC and Diffbind - beta
- COSMX - draft

bcbioR 0.1.3

fix duplicated gene names
Add combatseq
Add draft templates for TEAseq, COSMX
Adapt templates to nf-core rnaseq
Fix when sample start by number
Fix when rRNA rate is missing
Add by sample plots in QC
Add function to check nfcore samplesheet
Add PCA with variance analysis
Minor details fixed in QC RNAseq report
Correct metric for rRNA and tRNA

bcbioR 0.1.1

Add page to github
Make CHECK to pass
Add vignette