Search results

Filter #c not applying correctly

Status: Open.

#37 In plasslab/SCALPEL;

· JakobButler opened on Jun 16, 2026

The process ended before completion

bugSomething isn't workingSomething isn't working

can't reproduceThere is not enough information to reproduce this locally.There is not enough information to reproduce this locally.

Status: Open.

Bug

#36 In plasslab/SCALPEL;

· fzm311 opened on Apr 24, 2026

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

enhancementNew feature or requestNew feature or request

Status: Open.

#34 In plasslab/SCALPEL;

· Chris-Kato opened on Mar 9, 2026

stuck on salmon quant step

questionFurther information is requestedFurther information is requested

Status: Open.

#33 In plasslab/SCALPEL;

· nvivanco opened on Mar 4, 2026

Format of --clusters file

questionFurther information is requestedFurther information is requested

Status: Open.

#32 In plasslab/SCALPEL;

· guptas2005 opened on Feb 15, 2026

adding new samples

enhancementNew feature or requestNew feature or request

needs triage

Status: Open.

#31 In plasslab/SCALPEL;

· I-am-Shir opened on Feb 11, 2026

Issue Reading 10X GEX+ATAC Multiome Data

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

Status: Open.

#30 In plasslab/SCALPEL;

· guptas2005 opened on Feb 4, 2026

Unclear how to specify BAM files in sample sheet

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#29 In plasslab/SCALPEL;

· mschilli87 opened on Feb 2, 2026

The step for DGE and differential isoform usage is interrupted.

bugSomething isn't workingSomething isn't working

can't reproduceThere is not enough information to reproduce this locally.There is not enough information to reproduce this locally.

Status: Open.

#28 In plasslab/SCALPEL;

· Choeun-fran opened on Jan 26, 2026

Execution stops after skipping key processing steps

bugSomething isn't workingSomething isn't working

can't reproduceThere is not enough information to reproduce this locally.There is not enough information to reproduce this locally.

Status: Open.

#26 In plasslab/SCALPEL;

· Mangosteen24 opened on Dec 22, 2025

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

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#25 In plasslab/SCALPEL;

· mapostolides opened on Dec 12, 2025

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

questionFurther information is requestedFurther information is requested

staleThis is waiting for a response for a long time and it is not clear if it even is still relevant.This is waiting for a response for a long time and it is not clear if it even is still relevant.

Status: Open.

#23 In plasslab/SCALPEL;

· jinjinzh1190-cyber opened on Oct 16, 2025