/sccaf_example

The examples, data preprocessing and benchmark on parameters

Primary LanguageJupyter Notebook

sccaf_example

This repo includes all the jupyter notebooks used to process the datasets in the SCCAF project.

preprocessing

The folder preprocessing includes all the notebooks for data preprocessing.

reference-based_methods

The folder includes all the scripts to run the reference based cell type annotation methods that can read from the hdf5 files generated from the preprocessing notebooks. Here we include the reference based cell type annotation methods below:

Method Language URL
Logistic Regresion python SCCAF
SingleR R https://github.com/dviraran/SingleR
singleCellNet R https://github.com/pcahan1/singleCellNet
moana python https://github.com/yanailab/moana
ACTINN python https://github.com/mafeiyang/ACTINN
scClassify R https://sydneybiox.github.io/scClassify