Issues

• SEACells on Custom Dataset — Memory Issue During model.fit()

  dpeerlab/SEACells#81 · Filter by author dacon06 opened on Aug 1, 2025

• Is model.fit(min_iter=10, max_iter=1000) single-threaded? Can it be parallelized for faster

  dpeerlab/SEACells#80 · Filter by author wubaosheng opened on Jun 20, 2025

• Importing SEACells not possible - error creating env

  dpeerlab/SEACells#79 · Filter by author MichaelS27A opened on Apr 23, 2025

• SEACells Has no Attribute 'genescores'

  dpeerlab/SEACells#78 · Filter by author Branking24 opened on Apr 18, 2025
  1

• New version of SEACells no longer provides center of metacells?

  dpeerlab/SEACells#75 · Filter by author alifarhat40 opened on Feb 6, 2025

• Error fitting model on Jupyter lab via HPC cluster

  dpeerlab/SEACells#72 · Filter by author li-xuyang28 opened on Sep 29, 2024

• How to run SEACells efficiently on large-scale dataset

  dpeerlab/SEACells#70 · Filter by author koh2ng0 opened on Jul 22, 2024
  4

• What is the actual formula to construct the affinity kernel matrix?

  dpeerlab/SEACells#69 · Filter by author caodudu opened on Jul 15, 2024
  1

• CUDA error while running "model.fit"

  dpeerlab/SEACells#66 · Filter by author NekoClaviS opened on May 9, 2024

• Spurious metacell

  dpeerlab/SEACells#65 · Filter by author yxsee opened on May 6, 2024

• The data cannot be downloaded

  dpeerlab/SEACells#63 · Filter by author cfzgg opened on Apr 24, 2024
  1

• Handling metacell creation for rare cell types (<< 75 cells)

  dpeerlab/SEACells#61 · Filter by author uqzqiao opened on Apr 15, 2024
  1

• maxFragmentLength=147

  dpeerlab/SEACells#60 · Filter by author Aya-Balbaa opened on Apr 5, 2024

• Custom Neighborhood Graph for Metacells

  dpeerlab/SEACells#59 · Filter by author shahrozeabbas opened on Apr 1, 2024
  1

• No speed increase was observed when use_gpu=True

  dpeerlab/SEACells#58 · Filter by author OMIC-coding opened on Mar 28, 2024
  1

• Aggregation of expression data ends up in matrix filled with NaN's

  dpeerlab/SEACells#57 · Filter by author zvittorio opened on Jan 30, 2024
  6

• Scale or not scale be more suitable for computation of SEACells?

  dpeerlab/SEACells#56 · Filter by author NPTL1201 opened on Jan 4, 2024

• wonder why the @parm ceiling can be set to 10^9

  dpeerlab/SEACells#54 · Filter by author chenc327 opened on Nov 2, 2023

• [Question] Algorithm for PWM computation

  dpeerlab/SEACells#53 · Filter by author josephineyates opened on Oct 26, 2023

• Fail to install seacells via conda due to conflicts in environment.yaml

  dpeerlab/SEACells#52 · Filter by author ChangSuBiostats opened on Oct 5, 2023
  2

• cell-cell affinity matrix

  dpeerlab/SEACells#49 · Filter by author ytliu01 opened on Jul 15, 2023
  1

• Reproducibility issue

  dpeerlab/SEACells#48 · Filter by author evaham1 opened on Jul 8, 2023
  2

• Renaming the Seacells

  dpeerlab/SEACells#46 · Filter by author Gavin-Lijy opened on Jun 7, 2023
  1

• Many cells have zero non-trivial (>0.1) assignments

  dpeerlab/SEACells#43 · Filter by author simozhou opened on May 30, 2023
  1

• Issue with model.initialize_archetypes()

  dpeerlab/SEACells#41 · Filter by author iamsalil opened on May 18, 2023
  4