RTCGAToolbox
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see RTCGAToolbox.
A new tool for exporting TCGA Firehose data
Bioconductor version: 3.6
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 Kemal Samur
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
citation("RTCGAToolbox")):
Installation
To install this package, start R (version "3.4") 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
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Sequencing, Software |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | file LICENSE |
| Depends | R (>= 3.4.0) |
| Imports | Biobase, BiocGenerics, data.table (>= 1.9.4), GenomicRanges, GenomeInfoDb, httr, IRanges, limma(>= 3.18), methods, plyr, RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors, SummarizedExperiment, survival, XML |
| System Requirements | |
| URL | http://mksamur.github.io/RTCGAToolbox/ |
| Bug Reports | https://github.com/mksamur/RTCGAToolbox/issues |
See More
| Suggests | BiocStyle, Homo.sapiens, knitr, MultiAssayExperiment, readr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | CVE |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RTCGAToolbox_2.8.0.tar.gz |
| Windows Binary | RTCGAToolbox_2.8.0.zip |
| Mac OS X 10.11 (El Capitan) | RTCGAToolbox_2.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RTCGAToolbox |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RTCGAToolbox |
| Package Short Url | https://bioconductor.org/packages/RTCGAToolbox/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |