Issues

• How to construct lineage-associated or lineage-specific GRNs using CellOracle?

  morris-lab/CellOracle#245 · Filter by author wpf95 opened on Jun 14, 2026

• Information required on CellOracle perturbation scores interpretation

  morris-lab/CellOracle#244 · Filter by author mairamirza opened on May 11, 2026

• Request for Aedes aegypti mosquito genome

  morris-lab/CellOracle#243 · Filter by author milenamussmann opened on Mar 6, 2026

• Simulation of tissue-specific knockout/overexpression

  morris-lab/CellOracle#242 · Filter by author pavsol opened on Feb 12, 2026

• How to get inner product score for each cell?

  morris-lab/CellOracle#241 · Filter by author daisyyr opened on Dec 27, 2025

• Questions on simulating non-TF knockout

  morris-lab/CellOracle#239 · Filter by author lh12565 opened on Oct 22, 2025

• isolate after a pertubation its impasct on the different genes

  morris-lab/CellOracle#238 · Filter by author A-legac45 opened on Sep 5, 2025

• Are the p-values that are generated with get_links function adjusted for multiple testing?

  morris-lab/CellOracle#237 · Filter by author yasin-uzun opened on Sep 2, 2025

• Scalability Issues of CellOracle

  morris-lab/CellOracle#236 · Filter by author cconnors8 opened on Jul 24, 2025
  1

• how to used a snATACseq ARCHR already process in CellOralce

  morris-lab/CellOracle#235 · Filter by author A-legac45 opened on Jun 10, 2025
  1

• ImportError: celloracle/lib/python3.10/site-packages/velocyto/speedboosted.cpython-310-x86_64-linux-gnu.so: undefined symbol: __log10_finite

  morris-lab/CellOracle#234 · Filter by author WuMath opened on May 5, 2025

• velocyto broken and abandoned - switch to STARSolo?

  morris-lab/CellOracle#233 · Filter by author aowenson-imm opened on Apr 28, 2025

• Confusion in oracle.transition_prob

  morris-lab/CellOracle#232 · Filter by author Peg-Wu opened on Apr 23, 2025

• problem in interpreting network analysis result

  morris-lab/CellOracle#231 · Filter by author GGboy-Zzz opened on Apr 9, 2025

• Failed to build installable wheels for some pyproject.toml based projects (gimmemotifs)

  morris-lab/CellOracle#230 · Filter by author RyanLi2004-Bio opened on Mar 5, 2025
  1

• Pseudotime calculation using CytoTRACE

  morris-lab/CellOracle#229 · Filter by author yuxi010 opened on Feb 27, 2025

• Request for Populus trichocarpa Reference Genome

  morris-lab/CellOracle#228 · Filter by author KarenLRdePaiva opened on Feb 13, 2025

• plot_scores_as_rank , plotting don't seems to work ...;

  morris-lab/CellOracle#227 · Filter by author hamidsta opened on Feb 7, 2025

• Raw count import or normalized import

  morris-lab/CellOracle#225 · Filter by author CBannink opened on Jan 22, 2025
  1

• Failed to run ma.get_tss_info

  morris-lab/CellOracle#224 · Filter by author YangLi-Bio opened on Jan 18, 2025

• ma.SUPPORTED_REF_GENOME for new reference genome: soybean (Glycine max) William 82 v4

  morris-lab/CellOracle#223 · Filter by author YangLi-Bio opened on Jan 17, 2025

• Strange arrows after gene KO

  morris-lab/CellOracle#221 · Filter by author lh12565 opened on Nov 7, 2024

• ma.SUPPORTED_REF_GENOME for new chicken genome: GRCg7b

  morris-lab/CellOracle#220 · Filter by author YuJiandongBio opened on Nov 3, 2024

• Retrieving the multi dimensional gene expression shift vector

  morris-lab/CellOracle#219 · Filter by author CBannink opened on Oct 23, 2024

• network_analysis.linkList_to_networkgraph() Creates wrong directed edges

  morris-lab/CellOracle#218 · Filter by author osmanmerdan opened on Oct 16, 2024