rtracklayer
This is the development version of rtracklayer; for the stable release version, see rtracklayer.
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: Development (3.23)
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Maintainer: Michael Lawrence <lawremi at gmail.com>
citation("rtracklayer")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("rtracklayer")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Annotation, DataImport, Software, Visualization |
| Version | 1.69.1 |
| In Bioconductor since | BioC 2.2 (R-2.7) (17.5 years) |
| License | Artistic-2.0 + file LICENSE |
| Depends | R (>= 3.5), methods, GenomicRanges(>= 1.37.2) |
| Imports | XML (>= 1.98-0), BiocGenerics(>= 0.35.3), S4Vectors(>= 0.23.18), IRanges(>= 2.13.13), XVector(>= 0.19.7), Seqinfo, Biostrings(>= 2.77.2), curl, httr, Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) |
| System Requirements | |
| URL |
See More
| Suggests | GenomeInfoDb, BSgenome(>= 1.33.4), humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit |
| Linking To | S4Vectors, IRanges, XVector |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/rtracklayer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rtracklayer |
| Package Short Url | https://bioconductor.org/packages/rtracklayer/ |
| Package Downloads Report | Download Stats |