sci-dat

Sci-Download-Annotate-TCGA wraps around the API for TCGA and provides some simple interfaces for RNAseq, DNA methylation and clinical information from TCGA. These include downloading data from manifest files (also doing this in parallel), annotating the downloaded RNA and DNA methylation data with their clinical information and merging these dataframes to have a joint DNA methylation and RNAseq dataset (and adding information from biomart to these).

It is available under the GNU General Public License (Version 3).

Please post questions and issues related to sci-dat on the Issues section of the GitHub repository.

Running sci-dat

  1. Install sci-dat (Installing)

  2. View examples in Python or R (Examples)

  3. Look at CLI examples in (cli)

Extending sci-dat

  1. Make a pull request on github.