Lotfollahi-lab/nichecompass

Issues

• Problem creating NicheCompass model

  #74 opened 3 months ago by styounes
  2

• add minimal tests

  #49 opened 3 months ago by adamrboxall
  0

• add CLI to wrap 'reproducibility' scripts

  #50 opened 3 months ago by adamrboxall
  0

• deployment on HPC environments is difficult due to compatibility issues

  #53 opened 3 months ago by adamrboxall
  0

• clustering requires manual downstream processing, but is resource intensive

  #59 opened 3 months ago by adamrboxall
  0

• no way to export mu and std for active gps from the model conveniently

  #58 opened 3 months ago by adamrboxall
  0

• reference-query training cannot be performed with mismatched gene coverage

  #57 opened 3 months ago by adamrboxall
  0

• add simple model evaluation

  #55 opened 3 months ago by adamrboxall
  0

• Cannot replicate the result in the multimodal_tutorials

  #63 opened 3 months ago by dyxmvp
  3

• Kernel crashing when training the model with an adata (Visium HD) with 600k bins

  #71 opened 4 months ago by Rafael-Silva-Oliveira
  7

• Compatibility with Visium HD data (8 micron)

  #69 opened 4 months ago by Rafael-Silva-Oliveira
  4

• _compute_connectivities_umap

  #70 opened 4 months ago by mossishahi
  1

• installation requires pybedtools

  #67 opened 5 months ago by adamrboxall
  0

• ValueError: max() arg is an empty sequence [Error during the model training]

  #65 opened 6 months ago by hkeremcil
  6

• MERFISH sample without GPs

  #66 opened 6 months ago by Dana162001
  9

• Can I run NicheCompass with zebrafish Visium data?

  #64 opened 7 months ago by hkeremcil
  4

• reduce repo size

  #51 opened 10 months ago by adamrboxall
  0

• refactor run configuration

  #48 opened 10 months ago by adamrboxall
  0

• GP annotations files missing

  #56 opened a year ago by Eneritz
  0

• fix compatibility issues for development

  #46 opened a year ago by adamrboxall
  0