Issues

• Prioritize cREs for CRISPRi validation

  grnmultiome
  IGVF-UCSD/.github#16 · Filter by author adamklie opened on Mar 23, 2026
  3

• Repeat and expand variant effect predictions

  multiomes2fsnm3c
  IGVF-UCSD/.github#15 · Filter by author adamklie opened on Mar 23, 2026
  3

• Retrain CpGNet methylation models on new pseudobulk data

  s2fsnm3c
  IGVF-UCSD/.github#14 · Filter by author adamklie opened on Mar 23, 2026
  2

• Rebuild base-GRNs for SC-beta cell types

  grn
  IGVF-UCSD/.github#13 · Filter by author adamklie opened on Mar 23, 2026
  3

  

• Integrative analysis: snm3C-seq × Dominguez2020 bulk methylation

  integrationsnm3c
  IGVF-UCSD/.github#12 · Filter by author adamklie opened on Mar 23, 2026
  3

• Reprocess snm3C-seq with new samples

  snm3c
  IGVF-UCSD/.github#11 · Filter by author adamklie opened on Mar 23, 2026
  9

  

• Integrative analysis: igvf SC-islet Multiome × primary islet Multiome

  integrationmultiome
  IGVF-UCSD/.github#10 · Filter by author adamklie opened on Mar 23, 2026
  5

• Integrative analysis: igvf Multiome × Augsornworawat2023 Multiome

  integrationmultiome
  IGVF-UCSD/.github#9 · Filter by author adamklie opened on Mar 23, 2026
  5

• Begin v3 with IGVF uniform pipeline processed data

  infrastructuremultiome
  IGVF-UCSD/.github#8 · Filter by author adamklie opened on Mar 23, 2026
  13

  

• Identify gene modules correlated with INS secretion score and/or disease

  grnmultiome
  IGVF-UCSD/.github#7 · Filter by author adamklie opened on Mar 23, 2026
  3

• Upload v2 data to GCP

  infrastructuremultiome
  IGVF-UCSD/.github#6 · Filter by author adamklie opened on Mar 23, 2026
  5

  

• Finalize peak calling

  multiome
  IGVF-UCSD/.github#5 · Filter by author adamklie opened on Mar 23, 2026
  10

  

• Finalize DESeq2 pseudobulk methodology for RNA and ATAC

  multiome
  IGVF-UCSD/.github#4 · Filter by author adamklie opened on Mar 23, 2026
  13

  

• Recall peak-to-gene links using Gaulton lab pipeline

  multiome
  IGVF-UCSD/.github#2 · Filter by author adamklie opened on Mar 23, 2026
  3

• Retrain ChromBPNet models at different resolutions

  multiomes2f
  IGVF-UCSD/.github#1 · Filter by author adamklie opened on Mar 23, 2026
  16