Title: FAQ  
Owner: Former user
Creator: Former user 2011-10-18
Last Changed by: David Heiman 2018-10-24
Tiny Link: (useful for email) https://broadinstitute.atlassian.net/wiki/x/1INTMg
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Broad TCGA GDAC (4)
    Page: Analysis Run Release Notes
    Page: Documentation
    Page: Rationale for stddata Runs
    Page: Standardized Data Run Release Notes
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2018-10-24 11:03 David Heiman View Changes
2018-06-11 11:17 David Heiman View Changes
2018-04-17 07:43 Former user View Changes
2018-04-17 07:37 Former user View Changes
2018-03-09 12:54 Former user  
Outgoing Links
External Links (81)
    https://gdc.cancer.gov/resources-tcga-users/tcga-code-table…
    https://pypi.python.org/pypi/firebrowse/
    https://wiki.nci.nih.gov/display/TCGA/Platform#Platform-Pla…
    en.wikipedia.org/wiki/WinRAR
    https://confluence.broadinstitute.org/gdac.broadinstitute.o…
    genomics.unc.edu/projects/tcga.html
    gdac.broadinstitute.org/
    firebrowse.org/api-docs/#!/Archives
    https://tcga-data.nci.nih.gov/annotations
    en.wikipedia.org/wiki/Tar_(computing)
    firebrowse.org/api-docs/#!/Metadata/Patients
    https://confluence.broadinstitute.org/display/GDAC/Rational…
    firebrowse.org/viewGene.html?gene=erbb2
    cancergenome.nih.gov/
    https://confluence.broadinstitute.org/display/GDAC/fbget
    https://confluence.broadinstitute.org/display/GDAC/Download
    en.wikipedia.org/wiki/Gzip
    gdac.broadinstitute.org/runs/analyses__2015_04_02/data/ACC-…
    https://gdc-portal.nci.nih.gov/
    gdac.broadinstitute.org/runs/stddata__latest/samples_report…
    dx.doi.org/10.1038/nature12213
    https://www.biostars.org/p/93395/
    https://confluence.broadinstitute.org/download/attachments/…
    https://confluence.broadinstitute.org/display/GDAC/Standard…
    firebrowse.org/iCoMut/?cohort=acc
    https://wiki.nci.nih.gov/pages/viewpage.action?pageId=70812…
    cancergenome.nih.gov/cancersselected/acutemyeloidleukemia
    firebrowse.org
    firebrowse.org/
    dx.doi.org/10.1186/1471-2105-12-323
    https://confluence.broadinstitute.org/display/GDAC/Document…
    www.broadinstitute.org/cancer/cga/copynumber_pipeline
    https://wiki.nci.nih.gov/display/TCGA/TCGA+MAF+Files
    https://confluence.broadinstitute.org/display/GDAC/Analysis…
    cancergenome.nih.gov/cancersselected/melanoma
    https://gdc.nci.nih.gov/
    https://tcga-data.nci.nih.gov/docs/publications/tcga/
    https://gdc-portal.nci.nih.gov/projects/t
    https://confluence.broadinstitute.org/display/GDAC/Contact+…
    https://confluence.broadinstitute.org/display/GDAC/AWG+Runs
    firebrowse.org/api/v1/Metadata/Cohorts?format=json
    https://wiki.nci.nih.gov/display/TCGA/TCGA+Encyclopedia
    gdac.broadinstitute.org/runs/info/DOIs__stddata.html
    https://wiki.nci.nih.gov/display/TCGA/Batch
    tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp
    mailto:tcga@mail.nih.gov
    www.broadinstitute.org/igv/
    https://confluence.broadinstitute.org/display/GDAC/Dashboar…
    https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+F…
    https://confluence.broadinstitute.org/display/GDAC/Analysis…
    www.nature.com/nature/journal/v505/n7484/full/nature12912.h…
    www.cancer.gov/about-nci/organization/ccg
    https://confluence.broadinstitute.org/display/GDAC/Standard…
    https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode
    https://confluence.broadinstitute.org/display/GDAC/Dashboar…
    https://github.com/mariodeng/FirebrowseR
    mailto:genomics@broadinstitute.org
    www.broadinstitute.org/cancer/cga/mutsig
    genomics.broadinstitute.org/
    firebrowse.org/api-docs/#!/Metadata
    en.wikipedia.org/wiki/Md5sum
    gdac.broadinstitute.org/runs/analyses__latest/reports/
    bit.ly/mut-data-flow
    en.wikipedia.org/wiki/Digital_object_identifier
    https://gdc-portal.nci.nih.gov/legacy-archive/search/f
    https://web.archive.org/web/20140523030108/https://wiki.nci…
    firebrowse.org/api-docs/#!/Analyses
    gdac.broadinstitute.org/runs/analyses__latest/ingested_data…
    gatkforums.broadinstitute.org/discussion/4231/what-is-the-o…
    dx.doi.org/10.1038/nmeth.1226
    https://wiki.nci.nih.gov/display/TCGA/File+Format+Specifica…
    gdac.broadinstitute.org
    https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftp…
    genome.ucsc.edu/cgi-bin/hgTables
    https://wiki.nci.nih.gov/x/VxNCB
    gdac.broadinstitute.org/Analyses-DAG.html
    tcpaportal.org/
    firebrowse.org/api-docs/
    gdac.broadinstitute.org/runs/analyses__latest/reports
    https://docs.google.com/document/d/171JBve6xuz9ikWfRmfyBmg2…
    https://confluence.broadinstitute.org/display/GDAC/Standard…
Broad TCGA GDAC (13)     Page: Draft Analysis Run Notes
    Page: Analysis Run Release Notes
    Page: FAQ
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