TCGAutils
TCGA utility functions for data management
Bioconductor version: Release (3.17)
A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.
Author: Marcel Ramos [aut, cre] 
, Lucas Schiffer [aut], Sean Davis [ctb], Levi Waldron [aut]
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
citation("TCGAutils")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAutils")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("TCGAutils")| TCGAutils Essentials | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Preprocessing, Software, WorkflowStep |
| Version | 1.20.2 |
| In Bioconductor since | BioC 3.7 (R-3.5) (5.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 |
| Linking To | |
| Suggests | AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox(>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/waldronlab/TCGAutils/issues |
See More
| Depends On Me | |
| Imports Me | cBioPortalData, RTCGAToolbox, terraTCGAdata |
| Suggests Me | CNVRanger, curatedTCGAData, dce, glmSparseNet, IntOMICS |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TCGAutils_1.20.2.tar.gz |
| Windows Binary | TCGAutils_1.20.2.zip |
| macOS Binary (x86_64) | TCGAutils_1.20.2.tgz |
| macOS Binary (arm64) | TCGAutils_1.20.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TCGAutils |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TCGAutils |
| Bioc Package Browser | https://code.bioconductor.org/browse/TCGAutils/ |
| Package Short Url | https://bioconductor.org/packages/TCGAutils/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |