Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-TCGA
Curated list of TCGA resources
https://github.com/IARCbioinfo/awesome-TCGA
Last synced: 4 days ago
JSON representation
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Official links
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General informations
- NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.
- Data documentation - Describe how the data is generated, in particular the details of the bioinformatics pipeline used.
- NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.
- NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.
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Data repositories
- GDC homepage
- GDC data documentation
- GDC data release notes
- GDC legacy archive - The legacy data is the original data that uses the old genome build (hg19) as produced by the original submitter. The legacy data is not actively being updated in any way. Users should migrate to the harmonized data.
- List of cohorts with sample sizes - Shortcut to the GDC data portal with the list of all cancer sites with the number of cases and the number of available cases per data category.
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Downloading the data
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Official tools
- GDC data transfert tool - Official command line tool, see [here](https://github.com/IARCbioinfo/GDC-tricks) for a nice tutorial.
- GDC API - Official HTTP API. Note the [BAM Slicing](https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/) that can be quite useful.
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Broad Institute GDAC
- Python and UNIX wrappers
- Firebrowse - A web UI to visualise the results of the analyses performed by Firehose.
- Firebrowse - A web UI to visualise the results of the analyses performed by Firehose.
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Others
- GenomicDataCommons - A R/Bioconductor package for querying, accessing, and mining genomic datasets available from the GDC.
- TCGABiolinks - A R/Bioconductor package to search, download and prepare relevant data for analysis in R. Very powerful and well documented.
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Cloud computing
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Others
- Cancer Genomics Cloud - Developed by [Seven Bridges Genomics](https://www.sevenbridges.com). They have a [blog](https://www.sevenbridges.com/blog/) with useful case studies.
- FireCloud - Developed by the BROAD Institute.
- ISB Cancer Genomics Cloud - Developed by the Institute for Systems Biology in Seattle.
- ISB Cancer Genomics Cloud - Developed by the Institute for Systems Biology in Seattle.
- ISB Cancer Genomics Cloud - Developed by the Institute for Systems Biology in Seattle.
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Pan-TCGA analyses
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Others
- Tumor Fusion Gene Data Portal - 9,966 tumor samples from 33 TCGA cancer types and 689 normal samples in 19 TCGA normal tissue types were analyzed by PRADA pipeline and the realigned BAM files of RNAseq data.
- DriverDBv2 - WES and RNA-seq reanalysis to identify driver genes. Provides a nice graphical summary of mutation clustering in genes (e.g. for *[TP53](http://driverdb.tms.cmu.edu.tw/driverdbv2/gene_data_p.php?genename=TP53&geneproteinid=&submit=submit)*).
- BioXpress - RNA-seq-derived gene expression database, including TCGA among others.
- ASCAT Ploidy and Purity Estimates - [COSMIC](http://cancer.sanger.ac.uk/cosmic) hosts a tab separated table listing the ploidy and aberrant cell fraction (purity estimate), for TCGA samples re-analysed using ASCAT.
- ASCAT Ploidy and Purity Estimates - [COSMIC](http://cancer.sanger.ac.uk/cosmic) hosts a tab separated table listing the ploidy and aberrant cell fraction (purity estimate), for TCGA samples re-analysed using ASCAT.
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Publications
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Others
- Publication from Seven Bridges Genomics
- TCGABiolinks - Paper describing the R TCGABiolinks package.
- FirebrowseR - Paper describing the R FirebrowseR package.
- GenomicDataCommons - Paper describing the R GenomicDataCommons package.
- DriverDBv2
- ChimerDB - A new paper is in press for v3.0 according to rcsb.ewha.ac.kr/fusiongene.
- BioXpress
- TCGABiolinks - Paper describing the R TCGABiolinks package.
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