Datasets, Portals and Tools
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