Issues

• write some recommendations for cut&run when Igs are not paired with IPs.

  bcbio/bcbioR#145 · Filter by author lpantano opened on Jul 8, 2025
  1

  

• migrate chipseq report to new version

  bcbio/bcbioR#142 · Filter by author lpantano opened on Apr 15, 2025

• need to add readme file to shiny app for singlecell QC

  bcbio/bcbioR#140 · Filter by author lpantano opened on Apr 4, 2025

• modify diffbind to be compatible with atacseq

  bcbio/bcbioR#137 · Filter by author lpantano opened on Mar 19, 2025
  3

  

• ChipSeq Documentation DE and QC

  bcbio/bcbioR#136 · Filter by author lpantano opened on Mar 19, 2025
  1

  

• final folder

  bcbio/bcbioR#122 · Filter by author Gammerdinger opened on Feb 27, 2025

• Use other platforms for test-data that are bigger

  Feature

  bcbio/bcbioR#118 · Filter by author lpantano opened on Feb 21, 2025
  

• add riboRatio metaddata column to scrna test data tiny.rds

  enhancement
  bcbio/bcbioR#112 · Filter by author abartlett004 opened on Feb 13, 2025

• Add methods for scATAC

  documentation
  Feature

  bcbio/bcbioR#92 · Filter by author lpantano opened on Feb 3, 2025

• DE for continuous variables

  enhancement
  bcbio/bcbioR#56 · Filter by author eberdan opened on Nov 13, 2024

• load metrics for non- mouse / human.

  bug
  bcbio/bcbioR#55 · Filter by author eberdan opened on Nov 12, 2024
  1

• evaluate using chipseq qc template for cutandrun output

  enhancement
  bcbio/bcbioR#51 · Filter by author abartlett004 opened on Oct 11, 2024

• test and potentially make templates for cell type annotation

  bcbio/bcbioR#50 · Filter by author abartlett004 opened on Sep 23, 2024

• Options for GRN with single cell

  enhancement
  bcbio/bcbioR#49 · Filter by author lpantano opened on Sep 9, 2024

• DEseq report discussion

  documentationenhancementRNAseq
  bcbio/bcbioR#45 · Filter by author lpantano opened on Aug 22, 2024

• Adapt chipseq report to cutandrun output

  bcbio/bcbioR#43 · Filter by author abartlett004 opened on Aug 7, 2024
  3

• add checks for low count genes?

  bcbio/bcbioR#35 · Filter by author eberdan opened on Jun 24, 2024

• make sanitize_datatable into package function

  bcbio/bcbioR#29 · Filter by author abartlett004 opened on May 31, 2024

• check samplesheet function to ensure files exist

  enhancementRNAseq
  bcbio/bcbioR#27 · Filter by author abartlett004 opened on May 28, 2024

• Common repository for lists of protein coding genes

  bcbio/bcbioR#18 · Filter by author lpantano opened on May 8, 2024

• Common repository (dropbox?) for annotations to add to DE lists

  bcbio/bcbioR#17 · Filter by author lpantano opened on May 8, 2024

• similar projects

  question
  bcbio/bcbioR#13 · Filter by author lpantano opened on Apr 26, 2024

• Interactive volcano plot with glXYPlot

  enhancementRNAseq
  bcbio/bcbioR#12 · Filter by author upendrabhattarai opened on Apr 25, 2024

• Enrichment analysis flexibility

  enhancementRNAseq
  bcbio/bcbioR#11 · Filter by author lpantano opened on Apr 25, 2024

• DE - coefficient vs contrasts

  enhancementRNAseq
  bcbio/bcbioR#8 · Filter by author lpantano opened on Apr 25, 2024