A Modular Suite of Snakemake-based workflows for analysis of cancer genome data

LCR-modules

Binary classification of cancer samples from gene expression data

PRPS¹

Infering clustered mutations from many cancer genomes

Rainstorm/Doppler²

Error suppression and variant calling from duplex sequencing libraries

Dellingr³

Cancer Genomics Toolkit for Galaxy

tools_morinlab⁴

Read and somatic variant simulator

JARS

Publications using this software

1. Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma
2. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma
3. Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits
4. Enhancing knowledge discovery from cancer genomics data with Galaxy

Data Sets

• 73 paired de novo DLBCL genomes
• 30 paired relapsed/refractory DLBCL exomes

Contributors

• Chris Rushton
• Bruno Grande
• Prasath Pararajalingam
• Aixiang Jiang
• Marco Albuquerque
• Elie Ritch
• Selin Jessa