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