UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis

stefanie · September 6, 2019, 1:41am

"The UCSC Xena platform provides an unprecedented resource for public omics data from big projects like The Cancer Genome Atlas (TCGA), however, it is hard for users to incorporate multiple datasets or data types, integrate the selected data with popular analysis tools or homebrewed code, and reproduce analysis procedures. To address this issue, we developed an R package UCSCXenaTools for enabling data retrieval, analysis integration and reproducible research for omics data from the UCSC Xena platform.

In this technote we will outline how to use the UCSCXenaTools package to pull gene expression and clinical data from UCSC Xena for survival analysis."

…
Read the full Tech Note: https://ropensci.org/technotes/2019/09/06/ucscxenatools-surv/

ShixiangWang · September 6, 2019, 6:46am

@stefanie Thank you for editing this technote and improving English!

This technote is updated recently at UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis - Shixiang Wang

Topic		Replies	Views
A research compendium and methylation raw data General Q&A r , data , package , reproducibility	4	1879	September 30, 2017
Recommended R package (or tools) to facilitate possible search strings in systematic Literature Search (systematic literature review?) Package Use Questions	4	3440	October 9, 2019
A rentrez paper, and how to use the NCBI's new API keys Blog r , literature , community , ncbi , data-access	0	660	March 20, 2018
Feedback on text mining in rcrossref package Package Use Questions	0	1273	January 16, 2015
Searchable metadata in help files with htmlwidgets UseCases documentation	8	4219	August 29, 2018

UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis

Related Topics