Datasets

Datasets, Portals and Tools

Useful Cancer Genomics Data Portals and Sites:

Broad Institute TCGA copy number portal: Links to copy number profiles for over 10,000 cancers.
- The Integrative Genomics Viewer (IGV) is the browser. Data used in Zack et al., Nature Genetics, 2013, and multiple TCGA cancer marker papers.
- Tumorscape: Data for Beroukhim et al., Nature, 2010 with copy number profiles for ~3,000 cancers, now available within the Broad copy number portal, under '2011-02-01 Tumorscape'.
Tumorportal: Website with cancer mutation data for over 4,000 cancers, from Lawrence et al., Nature, 2014.
TCGA central data portal
dbGAP: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1
GTEx: http://www.gtexportal.org/home/
COSMIC: http://cancer.sanger.ac.uk/cosmic
DepMap: https://depmap.org/portal/
Gene Pattern: http://www.broadinstitute.org/cancer/software/genepattern/
cBioPortal: http://www.cbioportal.org/
International Cancer Genome Consortium: https://icgc.org/
The Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geo/
The UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGateway
Genomic Data Commons: home page and data portal

Meyerson Lab Tools

virID: https://github.com/jnoms/virID
ASCETS: https://github.com/beroukhim-lab/ascets
GATK PathSeq: All GATK tools available here, Meyerson lab members have contributed to PathSeq

Meyerson Lab Datasets for Pathogen Discovery Projects:

Meyerson Lab Datasets for Cancer Genome Analysis Projects: