ccle_extractor

Extracting gene expression datasets from CCLE database.

Manual installation of package requirements

Language	Packages
Python >= 3.7	pandas, matplotlib, seaborn
R	biomaRt, dplyr, edgeR

CCLE Data

• CCLE_RNAseq_rsem_genes_tpm_20180929.txt.gz
• Cell_lines_annotations_20181226.txt
• CCLE_RNAseq_genes_counts_20180929.gct.gz

Usage

from ccle.database import CancerCellLineEncyclopedia as CCLE

# Set gene_nemes
# Set ccle_names or cell_lines

selected_CCLE_subset = CCLE(
    gene_names = ['EGFR', 'ERBB2', 'ERBB3', 'ERBB4'],
    ccle_names = ['MCF7_BREAST', 'MDAMB231_BREAST']
)

''' or
selected_CCLE_subset = CCLE(
    gene_names = ['EGFR', 'ERBB2', 'ERBB3', 'ERBB4'],
    cell_lines = ['MCF7', 'MDA-MB-231']
)
'''

# GeneCards link (https://www.genecards.org)
selected_CCLE_subset.to_gene_summary()
# TPM value
selected_CCLE_subset.to_gene_expression()

Installation

$ git clone https://github.com/okadalabipr/ccle_extractor.git

License

MIT