{"repo":"ropensci/UCSCXenaTools","free":true,"listed":false,"github":"https://github.com/ropensci/UCSCXenaTools","clone":"git clone https://github.com/ropensci/UCSCXenaTools.git","description":":package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/","language":"R","stars":118,"topics":["ucsc-xena","downloader","api-client","tcga","ccle","icgc","ucsc","toil","treehouse","r"],"license":"GPL-3.0","category":"api-integrations-sdks","readme_excerpt":"UCSCXenaTools UCSCXenaTools is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Public omics data from UCSC Xena are supported through multiple turn-key Xena Hubs , which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. Who is the target audience and what are scientific applications of this package? - Target Audience: cancer and clinical researchers, bioinformaticians - Applications: genomic and clinical analyses Table of Contents - Installation - Data Hub List - Basic usage - Citation - How to contribute - Acknowledgment Installation Install stable release from r-universe/CRAN with: You can also install devel version of UCSCXenaTools from github with: If you want to build vignette in local, please add two options: Data Hub List All datasets are available at . Currently, UCSCXenaTools supports the following data hubs of UCSC Xena. - UCSC Public Hub: - TCGA Hub: - GDC Xena Hub: - ICGC Xena Hub: - Pan-Cancer Atlas Hub: - UCSC Toil RNAseq Recompute Compendium Hub: - PCAWG Xena Hub: - ATAC-seq Hub: - Treehouse Xena Hub: - … Users can update dataset list from the newest version of UCSC Xena by hand with XenaDataUpdate() function, followed by restarting R and library(UCSCXenaTools) . If any url of data hub is changed or a new data hub is online, please remind me by emailing t","default_branch":null,"files":null,"tree":[],"storefront":"/r/ropensci","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/ropensci/UCSCXenaTools/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}