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RTCGAToolbox

A new tool for exporting TCGA Firehose data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("RTCGAToolbox")):

Installation

To install this package, start R (version "4.3") 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")
RTCGAToolbox Tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, Sequencing, Software
Version 2.32.1
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-2
Depends R (>= 4.3.0)
Imports BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors(>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils(>= 1.9.4), utils
System Requirements
URL http://mksamur.github.io/RTCGAToolbox/
Bug Reports https://github.com/mksamur/RTCGAToolbox/issues
See More
Suggests BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me cBioPortalData, TCGAWorkflow
Suggests Me TCGAutils
Links To Me
Build Report Build Report

Package Archives

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

Source Package RTCGAToolbox_2.32.1.tar.gz
Windows Binary RTCGAToolbox_2.32.1.zip
macOS Binary (x86_64) RTCGAToolbox_2.32.1.tgz
macOS Binary (arm64) RTCGAToolbox_2.32.1.tgz
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 3.18 Source Archive