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.
- 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)