Issues

• comparing TF activity changes pre/post-knockout across multiple cell lines using run_ulm and limma

  saezlab/decoupleR#177 · Filter by author attaff opened on Nov 15, 2025

• Use multiple versions of OmnipathR

  saezlab/decoupleR#176 · Filter by author mhurtado13 opened on Nov 5, 2025

• Deciding to use a batch corrected matrix in with decoupleR::run_ulm

  saezlab/decoupleR#175 · Filter by author Rose-Hedderman opened on Sep 8, 2025

• Handling of duplicated gene symbols in run_ulm()

  saezlab/decoupleR#174 · Filter by author kakaka1221 opened on Sep 3, 2025

• decoupleR::get_progeny fails

  saezlab/decoupleR#173 · Filter by author ZZQ-1117 opened on Aug 22, 2025
  3

• Confirm DoRothEA confidence level in CollecTRI

  saezlab/decoupleR#172 · Filter by author liezeltamon opened on Aug 11, 2025

• TF all down-regulated in a cluster after rankby group.

  saezlab/decoupleR#171 · Filter by author wariobrega opened on Aug 7, 2025

• Clustering Based on TF Activity

  saezlab/decoupleR#170 · Filter by author TalaNoun opened on Jul 28, 2025

• URLError: <urlopen error [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1017)>

  saezlab/decoupleR#169 · Filter by author king2306-s opened on Jul 25, 2025

• Package dependencies not installed

  saezlab/decoupleR#168 · Filter by author JABioinf opened on Jul 25, 2025
  3

• Recent versions here are well behind those available from bioconductor?

  saezlab/decoupleR#167 · Filter by author jefferys opened on Jul 16, 2025
  2

• decoupleR::get_collectri [WARNING]

  saezlab/decoupleR#166 · Filter by author maartenciers opened on Jun 6, 2025
  1

• Problem with Organism in get_collectri

  saezlab/decoupleR#164 · Filter by author Estella-1017 opened on May 15, 2025
  3

• Comparing results from multiple conditions

  saezlab/decoupleR#163 · Filter by author nagendraKU opened on Apr 28, 2025

• get_collectri unable to download

  saezlab/decoupleR#162 · Filter by author ptb999 opened on Apr 26, 2025
  13

• dorothea and collectri database

  saezlab/decoupleR#161 · Filter by author lili-damowang opened on Apr 24, 2025
  1

• Vignette confusion

  saezlab/decoupleR#160 · Filter by author eliasschwall opened on Apr 16, 2025
  2

• Can anyone explain these enrichment scores and how should we interpret this?

  question
  saezlab/decoupleR#159 · Filter by author wangmasonic20 opened on Apr 11, 2025
  

• Question: p-values adjusted for mutiple testing

  question
  saezlab/decoupleR#158 · Filter by author Ultimtebeginner opened on Mar 28, 2025
  1