Issues

• After successfully running bt.tl.fe_fazal2019(sdata, batch_size=50000), can I obtain which subcellular structure each transcript belongs to?

  YeoLab/bento-tools#191 · Filter by author zhoutianrui-tongji opened on Sep 17, 2025
  1

• [BUG] Installation issue: resolution-too-deep

  bug
  YeoLab/bento-tools#190 · Filter by author IcecreamArtist opened on Aug 27, 2025
  3

  

• bt.tl.fe_xia2019 or bt.tl.fe_fazal2019 error

  YeoLab/bento-tools#189 · Filter by author haipinghao opened on Jul 23, 2025
  1

• [BUG]Installation issue: ModuleNotFoundError: No module named 'setuptools.dep_util'

  bug
  YeoLab/bento-tools#187 · Filter by author haipinghao opened on Jul 1, 2025
  

• bt.pl.lp_genes(sdata_filter,annotate=35)

  bug
  YeoLab/bento-tools#186 · Filter by author Melody-cell opened on Jun 12, 2025
  

• bt.io.prep() --> AttributeError: 'dict' object has no attribute 'to_scale_vector'

  bug
  Bug

  YeoLab/bento-tools#180 · Filter by author amitjavilaventura opened on Mar 14, 2025
  2

  

• Installation Issues: ModuleNotFoundError: No module named 'distutils.msvccompiler'

  bugdependencies
  Bug

  YeoLab/bento-tools#178 · Filter by author Yangyizehui opened on Feb 18, 2025
  2

  

• Update dependencies to support python >= 3.12

  dependencies
  YeoLab/bento-tools#177 · Filter by author nklkhlr opened on Feb 7, 2025
  2

  

• Issues when reproducing the Main Guide

  bug
  YeoLab/bento-tools#176 · Filter by author wgmao opened on Jan 23, 2025
  1

  

• Deprecate RNAforest model

  YeoLab/bento-tools#170 · Filter by author ckmah opened on Dec 17, 2024
  2

• Extend shape features

  enhancement
  YeoLab/bento-tools#168 · Filter by author ckmah opened on Nov 23, 2024

• Contribution docs

  documentation
  YeoLab/bento-tools#167 · Filter by author ckmah opened on Nov 5, 2024
  

• SpatialData compat. for included datasets

  bugenhancement
  YeoLab/bento-tools#144 · Filter by author ckmah opened on Aug 5, 2024 · v2.1.4
  

• Data structure and assumptions

  documentation
  YeoLab/bento-tools#113 · Filter by author ckmah opened on Feb 21, 2024
  

• Refine fluxmap boundaries

  enhancement
  YeoLab/bento-tools#112 · Filter by author ckmah opened on Jan 24, 2024