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 0.3.1

• 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