GenomicCoordinates
This is the released version of GenomicCoordinates; for the devel version, see GenomicCoordinates.
Enhanced string parsing for genomic coordinates
Bioconductor version: Release (3.23)
Extends string parsing capabilities for genomic coordinates, supporting various formats including comma-separated numbers, space-delimited coordinates, and automatic detection of GRanges, GPos, and GInteractions objects.
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
citation("GenomicCoordinates")):
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("GenomicCoordinates")
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("GenomicCoordinates")| Introduction to GenomicCoordinates | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataRepresentation, GenomeAnnotation, Infrastructure, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5), GenomicRanges, IRanges |
| Imports | S4Vectors, Seqinfo, InteractionSet, methods, plyranges, plyinteractions |
| System Requirements | |
| URL | https://github.com/js2264/GenomicCoordinates |
| Bug Reports | https://github.com/js2264/GenomicCoordinates/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle |
| Linking To | |
| 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 | GenomicCoordinates_1.0.0.tar.gz |
| Windows Binary (x86_64) | GenomicCoordinates_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicCoordinates_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicCoordinates_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicCoordinates |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicCoordinates |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicCoordinates/ |
| Package Short Url | https://bioconductor.org/packages/GenomicCoordinates/ |
| Package Downloads Report | Download Stats |