boston123456 / cenpa-sdl

Uses DepMap datasets and tumor data to identify SDL partners of CENPA. In collaboration with the Basrai Group at NCI.

About

This project uses DepMap datasets and tumor data to identify SDL partners of CENPA and is conducted in collaboration with the Basrai Group at National Cancer Institute.

Usage

This repo requires conda. Install and activate the conda environment with:

conda env create -f environment.yml
conda activate CENPA-SDL

Download the raw data and generate output with:

snakemake all

The outputs include both the pan-cancer and tissue-specific analysis

Data

The data used for this analysis can be found in data/ which will contain:

• CCLE_RPKM.gct: RNAseq gene expression data for 1019 cancer cell lines (in RPKM), Cancer Cell Line Encyclopedia, the Broad Institute, released on January 2nd, 2019

• DepMap_CRISPR.csv: Genetic Dependency, CRISPR, Public 18Q4, CERES, the DepMap project, the Broad Institute, released in November 2018

• DepMap_RNAi.csv: Genetic Dependency, Combined RNAi, the DepMap project, the Broad Institute, released in November 2018

• DepMap_cell_line_metadata.csv: Cell line metadata about cell lines in the 18Q4 release, including mapping between DepMap ID and CCLE names, the DepMap project, the Broad Institute

• TCGA_data_ISLE.RData: Processed TCGA data from ISLE with information of 8479 samples. Information needed includes RNAseq for of 19001 genes and survival information (survival time in days + survival outcome in terms of alive or dead) of each sample.