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.
A tool for detection of somatic, subclonal, mosaic, and germline CNVs from sequencing
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.
GAIL (Gene-gene Association Inference based on biomedical Literature) is a web interface and database that allow investigation, visualization, and mining of human gene-gene networks based on the PubMed articles.
InGRiD (Integrative Genomics Robust iDentification of cancer subgroups) is a statistical approach to improve prediction of cancer subgroups and identification of key genes and pathways by integrating information from biological pathway databases.
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 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.
The BMEG is a Cancer Data integration Platform that utilizes methods collected from DREAM challenges and applied to large datasets, such as the TCGA, and makes them avalible for analysis using a high performance graph database
PDX Finder is a freely available resource that is integrating, archiving and disseminating information about Patient Derived Xenograft models and their associated data.
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.