boston_warm

What's Changed

• fix readme by @lpantano in #135

• bump to 0.4.4 by @lpantano in #141

  • init QC single cell #123
  • on disk seurat object #128
  • add gene name to count matrix bcbio/rnaseq-reports#8
  • Add style checks to rnaseq and singlecell repositories
  • Restructure singlecell readmes

Full Changelog: v0.4.3...v.0.4.4

boston_pie

• 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

boston_cold

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

boston_black

• Fix bugs in RNAseq
• Add function to set up library

fall_boston

• 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