CaSpER is published in Nature Communications: https://www.nature.com/articles/s41467-019-13779-x

CaSpER documentation is here: RMD file.

BAFExtract code is available here.

Tutorials

1. Yale meningioma Bulk RNA-Seq dataset R code

2. TCGA-GBM Bulk RNA-Seq dataset R code

3. TCGA-BRCA Bulk RNA-Seq dataset
   R code

4. GBM Single-cell RNA-Seq dataset R code

5. 10x Single-cell RNA-Seq dataset R code

Each run generally takes about 5-30 minutes.