Issues

• Integer overflow in merge_DGE_PRED.R when generating large isoform-by-cell matrices

  bug
  Bug

  plasslab/SCALPEL#38 · Filter by author Chenshanming-repo opened on Sep 15, 2026
  3

  

• Filter #c not applying correctly

  plasslab/SCALPEL#37 · Filter by author JakobButler opened on Jun 16, 2026
  1

  

• The process ended before completion

  bugcan't reproduce
  Bug

  plasslab/SCALPEL#36 · Filter by author fzm311 opened on Apr 24, 2026
  1

  

• Pipeline crash in compute_prob.R when transcriptomic_distance is positive (10x 3' data)

  enhancement
  plasslab/SCALPEL#34 · Filter by author Chris-Kato opened on Mar 9, 2026
  5

  

• stuck on salmon quant step

  question
  plasslab/SCALPEL#33 · Filter by author nvivanco opened on Mar 4, 2026
  

• Format of --clusters file

  question
  plasslab/SCALPEL#32 · Filter by author guptas2005 opened on Feb 15, 2026
  2

  

• adding new samples

  enhancementneeds triage
  plasslab/SCALPEL#31 · Filter by author I-am-Shir opened on Feb 11, 2026
  2

  

• Issue Reading 10X GEX+ATAC Multiome Data

  documentationenhancement
  plasslab/SCALPEL#30 · Filter by author guptas2005 opened on Feb 4, 2026
  6

  

• Unclear how to specify BAM files in sample sheet

  documentationenhancementquestion
  plasslab/SCALPEL#29 · Filter by author mschilli87 opened on Feb 2, 2026
  3

  

• The step for DGE and differential isoform usage is interrupted.

  bugcan't reproduce
  plasslab/SCALPEL#28 · Filter by author Choeun-fran opened on Jan 26, 2026
  11

  

• Execution stops after skipping key processing steps

  bugcan't reproduce
  plasslab/SCALPEL#26 · Filter by author Mangosteen24 opened on Dec 22, 2025
  3

  

• Better document that *_ipriming_sites.bed.tar.gz contains the same data as *.polyA.track

  documentation
  plasslab/SCALPEL#25 · Filter by author mapostolides opened on Dec 12, 2025
  4

  

• Solution for the problem of the10x Chromium 3' scRNA-seq data stuck in the "salmon_bulk_quantification" step

  questionstale
  plasslab/SCALPEL#23 · Filter by author jinjinzh1190-cyber opened on Oct 16, 2025
  7

  

• Using STARsolo Output

  enhancement
  plasslab/SCALPEL#22 · Filter by author I-am-Shir opened on Oct 5, 2025
  4