RTCGA.mutations
This is the released version of RTCGA.mutations; for the devel version, see RTCGA.mutations.
Mutations datasets from The Cancer Genome Atlas Project
Bioconductor version: Release (3.23)
Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot.
Author: Marcin Kosinski <m.p.kosinski at gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski at gmail.com>
citation("RTCGA.mutations")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RTCGA.mutations")
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("RTCGA.mutations")| Using RTCGA to download mutations data as included in RTCGA.mutations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation Data, ExperimentData |
| Version | 20151101.42.0 |
| License | GPL-2 |
| Depends | R (>= 3.2.0), RTCGA |
| Imports | |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/RTCGA/RTCGA/issues |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RTCGA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RTCGA.mutations_20151101.42.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RTCGA.mutations |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RTCGA.mutations |
| Package Short Url | https://bioconductor.org/packages/RTCGA.mutations/ |
| Package Downloads Report | Download Stats |