Downstream of scRNA analysis --- Scanpy

import scanpy as sc

Data structure

image.png

Main API and it's logic

1. sc.pp.blabla
   pp = preprocessing
   perform a basic transformation on the data matrix, i.e., the numpy array .X.
2. sc.tl.blabla
   tl = tools
   add annotation to the data, i.e., change pandas dataframe .var and .obs
3. sc.pl.blabla
   pl = plotting
   plot function, largely parallels the tl.* and a few of the pp.* functions

other API can be found in references.

Discussion

This data structure is a very classical bioinformatic data structure, which ensembles some in Bioconductor.

References
https://scanpy.readthedocs.io/en/stable/basic_usage.html