https://github.com/bcbio/bcbior - boston_pie

• migrate rnaseq templates to its own repo https://github.com/bcbio/bcbioR/issues/120
• add HD visium QC https://github.com/bcbio/bcbioR/issues/101
• add HD visum clustering https://github.com/bcbio/bcbioR/issues/102
• include code to generate files for DEGpattern https://github.com/bcbio/bcbioR/issues/116
• double code for single cell https://github.com/bcbio/bcbioR/issues/130
• adapt to QC to ATACseq https://github.com/bcbio/bcbioR/pull/133
• fix error in names https://github.com/bcbio/bcbioR/pull/132
• fix GSEA rnaseq error and styling code https://github.com/bcbio/rnaseq-reports/pull/2

- R
Published by lpantano over 1 year ago

https://github.com/bcbio/bcbior - boston_cold

Filter genes according biotype or gene name https://github.com/bcbio/bcbioR/pull/117 Add Visium HD QC https://github.com/bcbio/bcbioR/issues/101 https://github.com/bcbio/bcbioR/pull/115 Add degPattern template https://github.com/bcbio/bcbioR/pull/97 Collapse multiple params files https://github.com/bcbio/bcbioR/issues/65 Add rmaseq library links https://github.com/bcbio/bcbioR/issues/60 Fix version comparison https://github.com/bcbio/bcbioR/pull/104 Save log object in sc data https://github.com/bcbio/bcbioR/pull/105 More docs for clusters ids https://github.com/bcbio/bcbioR/pull/106

- R
Published by lpantano over 1 year ago

https://github.com/bcbio/bcbior - boston_black

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

- R
Published by lpantano over 1 year ago

https://github.com/bcbio/bcbior - 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

- R
Published by lpantano over 1 year ago