README.md
In cdiener/tcgar: A small helper package for using data from the Genomic Data Commons
tcgar
R package to read TCGA data and connect it to analysis pipelines (e.g. bioconductor).
News
TCGA has recently migrated all of its data to the Genomic Data Commons Portal.
This new version of tcgar now uses GDC for all data downloads. It supports the legacy
and new archive, however, the preloaded gene ID maps are based on the legacy archive.
Usage
Get and install the GDC Data Transfer Tool.
You can download data from within tcgar or by hand. tcgar uses a download manifest to download
large selections of data at once. To obtain the manifest go to the GDC data portal
or the legacy portal (to get the original TCGA data).
This will present tou with a nice UI to select the data set you want. After that click
on "Download Manifest" and save it to your disk. This is all you will need to download
data.
Currently implements download and parsing for:
- Clinical data for samples and patients
- RNASeq data (from level 3 files)
- Exon Expression data (HuEx)
cdiener/tcgar documentation built on May 13, 2019, 2:41 p.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
tcgar
R package to read TCGA data and connect it to analysis pipelines (e.g. bioconductor).
News
TCGA has recently migrated all of its data to the Genomic Data Commons Portal.
This new version of tcgar now uses GDC for all data downloads. It supports the legacy
and new archive, however, the preloaded gene ID maps are based on the legacy archive.
Usage
Get and install the GDC Data Transfer Tool.
You can download data from within tcgar or by hand. tcgar uses a download manifest to download
large selections of data at once. To obtain the manifest go to the GDC data portal
or the legacy portal (to get the original TCGA data).
This will present tou with a nice UI to select the data set you want. After that click
on "Download Manifest" and save it to your disk. This is all you will need to download
data.
Currently implements download and parsing for:
- Clinical data for samples and patients
- RNASeq data (from level 3 files)
- Exon Expression data (HuEx)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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