awesome-tcga
github.com/iarcbioinfo/awesome-tcga ↗Curated list of TCGA resources
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me general informations resources from awesome-tcga"
Installation instructions →What's inside
Pan-TCGA analyses
- ASCAT Ploidy and Purity Estimates
- BioXpress
RNA-seq-derived gene expression database, including TCGA among others.
- ChimerDB
A comprehensive database of fusion genes encompassing analysis of deep sequencing data (including TCGA) and manual curations.
- DriverDBv2
WES and RNA-seq reanalysis to identify driver genes. Provides a nice graphical summary of mutation clustering in genes (e.g. for
- Firehose
See
- 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.
Publications
- BioXpress
- ChimerDB
A new paper is in press for v3.0 according to rcsb.ewha.ac.kr/fusiongene.
- DriverDBv2
- FirebrowseR
Paper describing the R FirebrowseR package.
- GenomicDataCommons
Paper describing the R GenomicDataCommons package.
- Official publication list
Cloud computing
- Cancer Genomics Cloud
Developed by
- FireCloud
Developed by the BROAD Institute.
- ISB Cancer Genomics Cloud
Developed by the Institute for Systems Biology in Seattle.
Official links
- Data documentationGeneral informations
Describe how the data is generated, in particular the details of the bioinformatics pipeline used.
- GDC data documentationData repositories
- GDC data release notesData repositories
- GDC homepageData repositories
- GDC legacy archiveData repositories
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.
- Infographic summary of the projectGeneral informations
Downloading the data
- FirebrowseBroad Institute GDAC
A web UI to visualise the results of the analyses performed by Firehose.
- FirebrowseRBroad Institute GDAC
An R package to download directly the results of the analyses performed by Firehose in R.
- FirehoseBroad Institute GDAC
An R package to download directly the results of the analyses performed by Firehose in R.
- GDC APIOfficial tools
Official HTTP API. Note the
- GDC data transfert toolOfficial tools
Official command line tool, see
- GDC Spreadsheet Download ToolOthers
Tool to download clinical and/or biospecimen metadata for a given set of files in a tab-delimited format.
Showing a sample of 36 resources. View the full list on GitHub →