Issues

• Download v1 dGTEx samples for splice compendium

  UCSC-Treehouse/splicing-compendium#287 · Filter by author cindyeliang opened on Oct 28, 2026
  

• Infer strandedness of splice compendium samples

  UCSC-Treehouse/splicing-compendium#286 · Filter by author cindyeliang opened on Oct 26, 2026
  

• Add TARGET osteosarcomas to TARGET sample sheet for download

  UCSC-Treehouse/splicing-compendium#285 · Filter by author cindyeliang opened on Oct 26, 2026
  1

• Download of TARGET osteosarcomas

  UCSC-Treehouse/splicing-compendium#284 · Filter by author cindyeliang opened on Oct 26, 2026
  

• Add sample SRA ID to SRA sample sheet; handle downloads using sample ID instead of project ID

  UCSC-Treehouse/splicing-compendium#283 · Filter by author cindyeliang opened on Oct 26, 2026

• Script to rsync .bam and .bai files to archive/projects/celiang/splicing-2026

  UCSC-Treehouse/splicing-compendium#282 · Filter by author cindyeliang opened on Oct 26, 2026

• Addition of sample ID column to differential splicing results

  UCSC-Treehouse/splicing-compendium#281 · Filter by author cindyeliang opened on Oct 26, 2026

• Script to filter differentially spliced events by p-adj and dPSI values

  UCSC-Treehouse/splicing-compendium#280 · Filter by author cindyeliang opened on Oct 26, 2026

• Filter for differentially spliced events

  UCSC-Treehouse/splicing-compendium#279 · Filter by author cindyeliang opened on Oct 26, 2026
  

• make compendium test file

  UCSC-Treehouse/splicing-compendium#277 · Filter by author cindyeliang opened on Oct 14, 2026
  

• Obtain list of JAMA + CKCC2 samples in polyA compendium and on glacier, separated by collaborator

  UCSC-Treehouse/splicing-compendium#276 · Filter by author cindyeliang opened on Oct 14, 2026
  

• Download script for Treehouse PolyA compendium samples on SRA

  UCSC-Treehouse/splicing-compendium#274 · Filter by author cindyeliang opened on Oct 13, 2026

• Download more datasets for Treehouse Splice Compendium v2

  UCSC-Treehouse/splicing-compendium#273 · Filter by author cindyeliang opened on Oct 13, 2026
  

• Unify snakemake workflow

  UCSC-Treehouse/splicing-compendium#271 · Filter by author jashapiro opened on Sep 28, 2026

• reduce memory for 03-merge_separate_junctions.R

  UCSC-Treehouse/splicing-compendium#270 · Filter by author jashapiro opened on Sep 28, 2026

• make paths in scripts/04-merge_sample_psi.R more portable

  UCSC-Treehouse/splicing-compendium#262 · Filter by author cindyeliang opened on Sep 11, 2026
  3

  

• multithreading line may not be needed for merge junctions script

  UCSC-Treehouse/splicing-compendium#249 · Filter by author cindyeliang opened on Sep 3, 2026

• merge event splice tables from Shiba

  UCSC-Treehouse/splicing-compendium#248 · Filter by author cindyeliang opened on Sep 3, 2026
  1

  

• break psi merge step into one for each type of table

  UCSC-Treehouse/splicing-compendium#245 · Filter by author cindyeliang opened on Aug 31, 2026
  3

  

• final rule to zip or tarball merged PSI, junctions.bed, gtf

  UCSC-Treehouse/splicing-compendium#242 · Filter by author cindyeliang opened on Aug 28, 2026
  1

  

• (not a priority until after v1 is released and published) feature: cross-tissue comparison of PSI values for splice events

  UCSC-Treehouse/splicing-compendium#233 · Filter by author cindyeliang opened on Aug 20, 2026
  

• Clean up unused scripts before release

  UCSC-Treehouse/splicing-compendium#229 · Filter by author cindyeliang opened on Aug 19, 2026
  1

  

• Change location of log files produced by merge_results.smk

  UCSC-Treehouse/splicing-compendium#228 · Filter by author cindyeliang opened on Aug 18, 2026
  1

  

• zip all metadata that's not the final merged compendium metadata?

  UCSC-Treehouse/splicing-compendium#200 · Filter by author cindyeliang opened on Jul 28, 2026

• Create snakemake rules for bam2junc_RI_snakemake.py

  UCSC-Treehouse/splicing-compendium#159 · Filter by author cindyeliang opened on Jun 16, 2026
  3