txdbmaker
This is the development version of txdbmaker; for the stable release version, see txdbmaker.
Tools for making TxDb objects from genomic annotations
Bioconductor version: Development (3.24)
A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.
Author: H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], R. Castelo [ctb], M. Lawrence [ctb], I-Hsuan Lin [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], L. Shepherd [ctb]
Maintainer: H. Pagès <hpages.on.github at gmail.com>
citation("txdbmaker")):H. Pagès, M. Carlson, P. Aboyoun, S. Falcon, M. Morgan. txdbmaker: Tools for making TxDb objects from genomic annotations. doi:10.18129/B9.bioc.txdbmaker, R package version 1.9.0, https://bioconductor.org/packages/txdbmaker.
Generated from the package metadata; it may differ from the package's own citation.
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("txdbmaker")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("txdbmaker")| Making TxDb Objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | Artistic-2.0 |
| Depends | BiocGenerics, S4Vectors (>= 0.47.6), Seqinfo, GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4) |
| Imports | methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils (>= 1.7.1), GenomeInfoDb, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) |
| System Requirements | |
| URL | https://bioconductor.org/packages/txdbmaker |
| Bug Reports | https://github.com/Bioconductor/txdbmaker/issues |
See More
| Suggests | RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | mygene |
| Imports Me | ASpli, BgeeCall, casper, crisprDesign, crisprViz, customProDB, DegNorm, DOTSeq, ELViS, EpiTxDb, EventPointer, ExpHunterSuite, FRASER, geneLenDataBase, GenomicPlot, GenomicState, IntEREst, metaseqR2, OUTRIDER, proActiv, proBAMr, profileplyr, QuasR, RCAS, recoup, Rhisat2, RiboDiPA, ribosomeProfilingQC, RNAmodR, scafari, scanMiRApp, scruff, sitadela, trackViewer, TSSr, txcutr, tximeta, wavClusteR |
| Suggests Me | AnnotationHub, annotatr, BindingSiteFinder, Bioc.gff, bumphunter, BUSpaRse, DEXSeq, doubletrouble, eisaR, GenomicFeatures, GenomicRanges, ORFik, OrganismDbi, polyRAD, raer, recount, saseR, SplicingGraphs, SPLINTER, systemPipeR, systemPipeRdata |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | txdbmaker_1.9.0.tar.gz |
| Windows Binary (x86_64) | txdbmaker_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/txdbmaker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/txdbmaker |
| Package Short Url | https://bioconductor.org/packages/txdbmaker/ |
| Package Downloads Report | Download Stats |