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 Datasets for Pathogen Discovery Projects:

• Cord colitis: http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP018116​
• Colon genome discovery (16S rRNA sequences from human colon samples): http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000383

Meyerson Lab Datasets for Cancer Genome Analysis Projects:

• Pugh et al., Pleuropulmonary Blastoma: http://www.ncbi.nlm.nih.gov/bioproject/17411
• Ojesina et al., Cervical Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000600.v1.p1
• Neuroblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000467.v8.p1
• Medulloblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v2.p2
• Carcinoid: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000579.v1.p1
• Imielinski et al., Lung Adenocarcinoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000488.v2.p1
• Banerji et al., Breast Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000369.v1.p1​
• Metastatic Cancers:
  https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001417.v2.p1
• Pediatric Renal Medullary Carcinomas
  https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001800.v2.p1
• Castration Resistant Prostate Cancer​http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001577.v1.p1
• ​Neuroendocrine Tumors
  https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000579.v1.p1
• Solitary Fibrous Tumors
  https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1

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