dpeerlab/SEACells

Issues

• Excluding 1st dimension when computing SEACells on ATAC data

  #73 opened 3 months ago by kjtreese
  0

• Error fitting model on Jupyter lab via HPC cluster

  #72 opened 4 months ago by li-xuyang28
  0

• How to run SEACells efficiently on large-scale dataset

  #70 opened 6 months ago by koh2ng0
  2

• Error when model.construct_kernel_matrix: can SEACells be applied in python command line, not just in Jupyter?

  #71 opened 5 months ago by LiuCanidk
  0

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

  #57 opened a year ago by zvittorio
  5

• Circular import and GPU version

  #62 opened 5 months ago by GLking123
  1

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

  #69 opened 6 months ago by caodudu
  1

• The data cannot be downloaded

  #63 opened 9 months ago by cfzgg
  1

• CUDA error while running "model.fit"

  #66 opened 8 months ago by NekoClaviS
  0

• Spurious metacell

  #65 opened 8 months ago by yxsee
  0

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

  #61 opened 9 months ago by uqzqiao
  0

• maxFragmentLength=147

  #60 opened 10 months ago by Aya-Balbaa
  0

• Custom Neighborhood Graph for Metacells

  #59 opened 10 months ago by shahrozeabbas
  0

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

  #52 opened a year ago by ChangSuBiostats
  2

• No speed increase was observed when use_gpu=True

  #58 opened 10 months ago by OMIC-coding
  1

• Way too strict dependency pins

  #39 opened 2 years ago by Zethson
  3

• Issue with model.initialize_archetypes()

  #41 opened 2 years ago by iamsalil
  4

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

  #56 opened a year ago by NPTL1201
  0

• conda environment yaml file dependency seems conflict

  #55 opened a year ago by shiqi-yang
  1

• Reproducibility issue

  #48 opened 2 years ago by evaham1
  2

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

  #54 opened a year ago by chenc327
  0

• [Question] Algorithm for PWM computation

  #53 opened a year ago by josephineyates
  0

• Cannot initialize_archetypes

  #30 opened 2 years ago by GuiSeSanz
  3

• Computing SEACells on individual samples

  #40 opened 2 years ago by learning-MD
  1

• cell-cell affinity matrix

  #49 opened 2 years ago by ytliu01
  1

• Add pre-commit hooks

  #44 opened a year ago by WeilerP
  0

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

  #43 opened 2 years ago by simozhou
  1

• PWM for mouse genome

  #47 opened a year ago by torkencz
  1

• The data cannot be downloaded

  #50 opened a year ago by hai178912522
  1

• Renaming the Seacells

  #46 opened 2 years ago by Gavin-Lijy
  1

• model.fit hangs indefinitely

  #18 opened 2 years ago by smorabit
  12

• MemoryError when fitting model.fit

  #34 opened 2 years ago by tatyana-perlova
  10

• PWM.h5ad in SEACells/notebooks/SEACell_tf_activity.ipynb

  #42 opened 2 years ago by roshan9128
  2

• Gene-peak association fails with Cellranger GTF file

  #24 opened 2 years ago by jordanc17
  0

• RuntimeError: cannot cache function 'sparse_mean_var_minor_axis'

  #38 opened 2 years ago by simozhou
  2

• ValueError: row, column, and data array must all be the same length when running model.fit

  #37 opened 2 years ago by tatyana-perlova
  3

• gene score matrix with sparse format

  #23 opened 2 years ago by fl-yu
  1

• ArchR code tutorial - addGroupCoverage has no maxFragmentLength param

  #36 opened 2 years ago by simozhou
  0

• Issue with cupyx

  #31 opened 2 years ago by jindalk
  4

• Save Model

  #26 opened 2 years ago by Sayyam-Shah
  2

• Peak calling on NFR fragments

  #35 opened 2 years ago by ivanferrreira
  4

• Reproducible example for the PBMC dataset

  #32 opened 2 years ago by lebf3
  1

• Issues of model.initialize_archetypes

  #21 opened 2 years ago by fl-yu
  3

• R version of SEACells

  #33 opened 2 years ago by zji90
  1

• Different metacells gained when repeating analysis on same data set

  #16 opened 2 years ago by marie3003
  1

• SeaCells analysis for each cell type

  #25 opened 2 years ago by fl-yu
  1

• Multiome Dataset

  #22 opened 2 years ago by Sayyam-Shah
  4

• peak calling for each metacell

  #20 opened 2 years ago by fl-yu
  1

• Type checking needed in initialize_archetypes

  #17 opened 2 years ago by smorabit
  1

• Local paths in requirements.txt

  #15 opened 3 years ago by maxim-h
  3