RTCGAToolbox

DOI: 10.18129/B9.bioc.RTCGAToolbox  

A new tool for exporting TCGA Firehose data

Bioconductor version: Release (3.16)

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Author: Mehmet Samur [aut], Marcel Ramos [aut, cre] , Ludwig Geistlinger [ctb]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RTCGAToolbox")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RTCGAToolbox")

 

HTML	R Script	RTCGAToolbox Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, Sequencing, Software
Version	2.28.4
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 years)
License	GPL-2
Depends	R (>= 3.5.0)
Imports	BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, grDevices, httr, limma, methods, RaggedExperiment, RCircos, RCurl, RJSONIO, rvest, S4Vectors(>= 0.23.10), stats, stringr, SummarizedExperiment, survival, TCGAutils(>= 1.9.4), utils, XML
LinkingTo
Suggests	BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
SystemRequirements
Enhances
URL	http://mksamur.github.io/RTCGAToolbox/
BugReports	https://github.com/mksamur/RTCGAToolbox/issues
Depends On Me
Imports Me	cBioPortalData, TCGAWorkflow
Suggests Me	TCGAutils
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RTCGAToolbox_2.28.4.tar.gz
Windows Binary	RTCGAToolbox_2.28.4.zip
macOS Binary (x86_64)	RTCGAToolbox_2.28.4.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RTCGAToolbox
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTCGAToolbox
Bioc Package Browser	https://code.bioconductor.org/browse/RTCGAToolbox/
Package Short Url	https://bioconductor.org/packages/RTCGAToolbox/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive