The GEMINI package allows users to analyze combinatorial CRISPR screens, as described in Zamanighomi et al.
GEMINI package on Github: github.com/sellerslab/gemini
GEMINI package on Bioconductor: bioconductor.org/packages/devel/bioc/html/gemini.html
Drug sensitivity, shRNA knockdown, CRISPR-Cas9 knockout, splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cancer cell lines.
Broad Institute CCLE portal: portals.broadinstitute.org/ccle