CCLE_DataParser

Data parser for CCLE

 * filename  source/link
 * baseline expression: CCLE_expression.csv, source link: https://depmap.org/portal/download/ (19Q3: log2(RPKM+1))
 * baseline expression: CCLE_expression.csv, source link: https://depmap.org/portal/download/ (20Q1: log2(TPM+1))
 * mutation: CCLE_mutations.csv, source link: https://depmap.org/portal/download/
 * copy number variation: CCLE_gene_cn.csv, source link: https://depmap.org/portal/download/
 * cell line: sample_info.csv, source link: https://depmap.org/portal/download/
 * compound: , source link:
 * drug sensitivity: CCLE_NP24.2009_Drug_data_2015.02.24.csv, source link:
 * model list: https://cellmodelpassports.sanger.ac.uk/downloads

How to use it?

Download files listed above and put it in a folder (e.g., /data/DR/db/CCLE/):

DB_PATH = '/data/DR/db/CCLE/'
DB_FILE = {'MODEL':'model_list_20200204.csv',
           'EXP_tpm':'CCLE_expression.csv', # log2(TPM+1)
           'EXP_rpkm': 'CCLE_expression_log2RPKM.csv', # log2(RPKM+1)
           'CNV':'CCLE_gene_cn.csv',
           'MUT':'CCLE_mutations.csv',
           'RESP':'CCLE_NP24.2009_Drug_data_2015.02.24.csv',
           'CELL': 'sample_info.csv',
           'DRUG':''}

type $python useCCLE.py to generate the following files in a tidy format ready for analysis

gene expression: cell line by gene matrix
somatic mutation: cell line by gene matrix
copy number variation: cell line by gene matrix
drug sensitivity: compound by cell line matrix