Issues

• Permutation test yields significant p-values for random gene sets when using a weighted score

  broadinstitute/ssGSEA2.0#45 · Filter by author gregpoore opened on Aug 6, 2025
  3

• Division by Zero in ssGSEA2.0.R(Lines 453-455) for sum.correl.u = 0

  broadinstitute/ssGSEA2.0#42 · Filter by author rela-v opened on Jun 13, 2025

• object 'm' not found

  bug
  broadinstitute/ssGSEA2.0#39 · Filter by author ruzy99 opened on Apr 2, 2025
  1

• combine.mode = "combine.add"

  bug
  broadinstitute/ssGSEA2.0#38 · Filter by author Maj18 opened on Mar 29, 2025
  1

• Help with Error in parse_args (Using GenePattern for PTM-SEA)

  help wanted
  broadinstitute/ssGSEA2.0#37 · Filter by author orbi1234 opened on Mar 5, 2025
  1

• Number of cores in ssgsea-cli.R is hardcoded but should be set using command line arguments

  enhancement
  broadinstitute/ssGSEA2.0#33 · Filter by author sstein93 opened on Jul 15, 2024

• ssGSEA2 error in HPC environments when available cores is not equal to total number of cores.

  enhancement
  broadinstitute/ssGSEA2.0#32 · Filter by author cwlkr opened on Jun 13, 2024

• Error in ssGSEA2(input.ds = opt$input.ds, output.prefix = opt$output.prefix, : object 'm' not found

  bug
  broadinstitute/ssGSEA2.0#31 · Filter by author YuyingSuo opened on May 29, 2024

• How do I perform ssGSEA on single cell RNA seq data when it has already been preprocessed in Seurat version v5?

  help wanted
  broadinstitute/ssGSEA2.0#29 · Filter by author Saumya513 opened on Dec 26, 2023

• Optimal Gene Filtering for TPM Expression Data in RNA-seq Analysis: Impact of Non-Protein Coding Biotypes on Hallmark Enrichment Analysis

  help wanted
  broadinstitute/ssGSEA2.0#28 · Filter by author snijesh opened on Nov 29, 2023
  1