-omics

Gene Set Enrichment Analysis (GSEA) and Molecular Signatures Database (MSigDB)

GSEA is an open source software tool for the analysis of global transcription profiling data, available as a standalone desktop application and as GenePattern modules. The underlying method determines whether a given gene set, corresponding to a biological process, pathway, phenotype or cellular perturbation, is significantly coordinately up- or down-regulated and thus shed light on underlying mechanism. It can be used to compare phenotypes or used on individual samples. The software provides useful visualizations and reports for interpretation of results.

Patient-Specific Drug-Gene Networks for Recommending Targeted Cancer Therapies (CDGnet)

CDGnet is a tool for prioritizing targeted therapies based on an individual's tumor profile. Tumor molecular profiling refers to the use of a panel of genes and proteins that are assessed for potential abnormalities, including genetic changes and over/under expression of genes or proteins, in order to decide on targeted treatment plans. CDGnet incorporates information from biological networks relevant to the cancer type and to the specific alterations, FDA-approved targeted cancer therapies and indications, additional gene-drug information, and data on whether given genes are oncogenes.

Lancet

Local-assembly based somatic variant caller for short read sequencing data. Lancet detects somatic SNVs, indels, and more complex mutations by jointly analyzing reads from tumor and matched normal samples using colored de Bruijn graphs.

Globus

Globus software services provide secure cancer research data transfer, synchronization, and sharing in distributed environments at large scale. These services can be integrated into applications and research data gateways, leveraging Globus identity management, single sign-on, search, and authorization capabilities. Globus Genomics integrates Globus with the Galaxy genomics workflow engine and Amazon Web Services to enable cancer genomics analysis that can elastically scale compute resources with demand.

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