Bioc.gff
This is the development version of Bioc.gff; for the stable release version, see Bioc.gff.
Read and write GFF and GTF files
Bioconductor version: Development (3.24)
Parse GFF and GTF files using C++ classes. The package also provides utilities to read and write GFF3 files. The GFF (General Feature Format) format is a tab-delimited file format for describing genes and other features of DNA, RNA, and protein sequences. GFF files are often used to describe the features of genomes.
Author: Michael Lawrence [aut], Hervé Pagès [aut], Marcel Ramos [ctb], Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("Bioc.gff")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Bioc.gff")
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("Bioc.gff")| Bioc.gff: GFF3 File Format Support | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | BiocBaseUtils, BiocGenerics, BiocIO, curl, GenomicRanges, IRanges, methods, Rsamtools, S4Vectors, Seqinfo, stats, utils, XVector |
| System Requirements | |
| URL | https://github.com/Bioconductor/Bioc.gff |
| Bug Reports | https://github.com/Bioconductor/Bioc.gff/issues |
See More
| Suggests | BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData, knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Linking To | S4Vectors, XVector, IRanges |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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 | Bioc.gff_1.3.0.tar.gz |
| Windows Binary (x86_64) | Bioc.gff_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | Bioc.gff_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | Bioc.gff_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Bioc.gff |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Bioc.gff |
| Bioc Package Browser | https://code.bioconductor.org/browse/Bioc.gff/ |
| Package Short Url | https://bioconductor.org/packages/Bioc.gff/ |
| Package Downloads Report | Download Stats |