Skip to content

Utility functions for single cell analysis with scanpy.

Notifications You must be signed in to change notification settings

Marius1311/utility_functions

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

91 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

utility_functions

These are some utility funciton I found helpful in my data analysis tasks. Some of these are just copied from elsewhere, that's indicated in the scripts. Some others are super ugly because I haven't spend any time cleaning them up.

Contents

  • combat: combat funciton for batch effects, copied from Brent Pedersens github repo (https://github.com/brentp/combat.py). This will also be in scanpy soon, and in a much cleaner version
  • gp_de: fits Gaussian Processes to gene expression values sampled in pseudotime
  • cite_utils: some helper functions for working with cite seq data in scanpy
  • utils: some general utility funcitons. My personal highlight is a functions that creates nice interactive histograms that can be useful when looking for filtering thresholds
  • velocyto_utils: some utility funcitons for working with the Velocyto package, some of which are copied from their jupyter notebook github repo (https://github.com/velocyto-team/velocyto-notebooks/tree/master/python)

About

Utility functions for single cell analysis with scanpy.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Contributors 3

  •  
  •  
  •