gdac.broadinstitute.org

Broad GDAC Firehose

Cervical and endocervical cancers. Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. FFPE Pilot Phase II. Head and Neck squamous cell carcinoma. Pan-kidney cohort (KICH KIRC KIRP). Kidney renal clear cell carcinoma. Kidney renal papillary cell carcinoma. Brain Lower Grade Glioma. Lung squamous cell carcinoma. Stomach and Esophageal carcinoma. Testicular Germ Cell Tumors. Uterine Corpus Endometrial Carcinoma. Downloading data from this site constitutes agreement to TCGA data usage policy.

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Broad GDAC Firehose | gdac.broadinstitute.org Reviews

<META> DESCRIPTION

Cervical and endocervical cancers. Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. FFPE Pilot Phase II. Head and Neck squamous cell carcinoma. Pan-kidney cohort (KICH KIRC KIRP). Kidney renal clear cell carcinoma. Kidney renal papillary cell carcinoma. Brain Lower Grade Glioma. Lung squamous cell carcinoma. Stomach and Esophageal carcinoma. Testicular Germ Cell Tumors. Uterine Corpus Endometrial Carcinoma. Downloading data from this site constitutes agreement to TCGA data usage policy.

<META> KEYWORDS

1 rationale

2 mission statement

3 cga tools

4 how to cite

5 version info

6 firebrowse

7 dashboards

8 standard data

9 standard analyses

10 custom awg runs

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Broad GDAC Firehose | gdac.broadinstitute.org Reviews

https://gdac.broadinstitute.org

Cervical and endocervical cancers. Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. FFPE Pilot Phase II. Head and Neck squamous cell carcinoma. Pan-kidney cohort (KICH KIRC KIRP). Kidney renal clear cell carcinoma. Kidney renal papillary cell carcinoma. Brain Lower Grade Glioma. Lung squamous cell carcinoma. Stomach and Esophageal carcinoma. Testicular Germ Cell Tumors. Uterine Corpus Endometrial Carcinoma. Downloading data from this site constitutes agreement to TCGA data usage policy.

INTERNAL PAGES

gdac.broadinstitute.org

1

Analysis Overview -

http://gdac.broadinstitute.org/runs/analyses__latest/reports

28 January 2016 analyses 2016 01 28. Broad Institute/MD Anderson Cancer Center/Harvard Medical School. Broad Institute TCGA Genome Data Analysis Center (2016): Analysis Overview for 28 January 2016. Broad Institute of MIT and Harvard. doi:10.7908/C1K9371X. This is an overview of all analysis pipelines from Firehose run "28 January 2016". A total of 1528 reports are available for analysis run "28 January 2016". Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Brain Lower Grade Glioma.

2

Broad GDAC Firehose Analyses Workflow Graph

http://gdac.broadinstitute.org/Analyses-DAG.html

Broad Institute GDAC Firehose Analyses Workflow Graph. Last Updated: 2015 05 07. Below is a pictorial representation of the workflow Firehose executes upon each disease cohort in our standard Analyses runs. Clicking on a shaded rectangular node in this graph will bring you to the respective Nozzle report. For that analysis task. From that report you can also use the Related Reports feature. MiRseq Clustering Consensus Plus. MiRseq Clustering Consensus Plus. Aggregate Molecular Subtype Clusters. Correlate...

3

stddata__2016_01_28 Samples Report

http://gdac.broadinstitute.org/runs/stddata__latest/samples_report

Stddata 2016 01 28 Samples Report. There were 244 redactions, 3362 replicate aliquots, 23 blacklisted aliquots, and 481 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs. Summary of TCGA Tumor Data. Click on a tumor type to display a tumor type specific Samples Report. This figure depicts the distribution of available data on a per participant basis. This fi...

4

stddata__2016_07_15 Samples Report

http://gdac.broadinstitute.org/runs/sampleReports/latest

Stddata 2016 07 15 Samples Report. There were 244 redactions, 3365 replicate aliquots, 23 blacklisted aliquots, and 481 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs. Summary of TCGA Tumor Data. Click on a tumor type to display a tumor type specific Samples Report. This figure depicts the distribution of available data on a per participant basis. This fi...

5

TCGA GDAC Firehose clinical parameters map

http://gdac.broadinstitute.org/runs/info/clinical

This is an interactive heatmap of the current set of TCGA clinical data elements (CDEs) picked by Firehose for. Correlative analyses, broken down by disease cohort. Hovering over a cell will show the status of the given CDE. For that disease cohort. The GREEN/RED colors respectively mean that the given CDE was/wasn't available for the that cohort. Cervical carcinoma pelvic extension text. Date of initial pathologic diagnosis. Days to last followup. Days to last known alive. Days to submitted specimen dx.

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confluence.broadinstitute.org

Home - Broad TCGA GDAC - Broad Institute Confluence

https://confluence.broadinstitute.org/display/GDAC

Skip to header menu. Skip to action menu. Skip to quick search. Link to this Page…. Skip to end of metadata. Added by Aaron D. Ball. Last edited by David Heiman. On Feb 22, 2016 ( view change. Go to start of metadata. Searching Broad TCGA GDAC. VizDev Team Meeting Notes. As of December 2013 this is no longer the public-facing home page for the Broad GDAC Firehose pipeline. Please visit. For the Broad GDAC Firehose home page. Born of the desire to systematize analyses from The Cancer Genome Atlas. Perform...

confluence.broadinstitute.org

FireBrowse Release Notes - Broad TCGA GDAC - Broad Institute Confluence

https://confluence.broadinstitute.org/display/GDAC/FireBrowse+Release+Notes

Skip to header menu. Skip to action menu. Skip to quick search. Link to this Page…. Skip to end of metadata. Added by Michael Noble. Last edited by Michael Noble. On Aug 12, 2016 ( view change. Go to start of metadata. 1134 (2016 08 12). Deployed several new iCoMut instances in support of AWG analyses (TCGA credentials required to view). Boosted performance of some copy number API queries by creating additional indexes on the database backend. 1133 (2016 06 13). Fbget bindings v0.1.7. 1132 (2016 06 02).

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News | Caleydo

http://www.caleydo.org/news

12 Apr 2016 LineUp integrated in Microsoft PowerBI. Microsoft’s PowerBI platform makes data visualization accessible to a broad audience. We’re happy to see our LineUp tool integrated into PowerBI. As Table Sorter . It is exciting that one of our research prototypes has become part of a popular commercial product. See the tools page. For details about LineUp. 1 Mar 2016 Postdoc and software developer postions at Harvard Medical School. In the Department of Biomedical Informatics at Harvard Medical School.

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Broad GDAC Firehose

Cervical and endocervical cancers. Lymphoid Neoplasm Diffuse Large B-cell Lymphoma. FFPE Pilot Phase II. Head and Neck squamous cell carcinoma. Pan-kidney cohort (KICH KIRC KIRP). Kidney renal clear cell carcinoma. Kidney renal papillary cell carcinoma. Brain Lower Grade Glioma. Lung squamous cell carcinoma. Stomach and Esophageal carcinoma. Testicular Germ Cell Tumors. Uterine Corpus Endometrial Carcinoma. Downloading data from this site constitutes agreement to TCGA data usage policy.

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