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Bioconductor - txdbmaker (development version)

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 (3.22)

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], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], L. Shepherd [ctb]

Maintainer: H. Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("txdbmaker")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")
Details biocViews Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software Version 1.5.6 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License Artistic-2.0 Depends BiocGenerics, S4Vectors, Seqinfo, GenomicRanges(>= 1.61.1), GenomicFeatures(>= 1.61.4) Imports methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, 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, crisprDesign, crisprViz, customProDB, DegNorm, ELViS, EpiTxDb, FLAMES, GenomicPlot, IntEREst, metaseqR2, ORFik, OUTRIDER, proActiv, proBAMr, QuasR, RCAS, recoup, Rhisat2, RiboDiPA, ribosomeProfilingQC, RNAmodR, scanMiRApp, scruff, sitadela, trackViewer, txcutr, tximeta, GenomicState, geneLenDataBase Suggests Me AnnotationHub, BindingSiteFinder, bumphunter, BUSpaRse, DEXSeq, doubletrouble, eisaR, GenomicFeatures, GenomicRanges, OrganismDbi, raer, recount, SplicingGraphs, SPLINTER, systemPipeR Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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