RTCGAToolbox
This is the development version of RTCGAToolbox; for the stable release version, see RTCGAToolbox.
A new tool for exporting TCGA Firehose data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("RTCGAToolbox")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Sequencing, Software |
| Version | 2.37.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 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_2.37.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |