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txdbmaker

Tools for making TxDb objects from genomic annotations


Bioconductor version: Release (3.19)

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], 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 "4.4") and enter:


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

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 PDF
NEWS Text

Details

biocViews Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends BiocGenerics, S4Vectors, GenomeInfoDb(>= 1.39.9), GenomicRanges, GenomicFeatures
Imports methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, 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, mirbase.db, ensembldb, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me mygene
Imports Me ASpli, crisprDesign, crisprViz, customProDB, DegNorm, EpiTxDb, FLAMES, GenomicPlot, IntEREst, metaseqR2, ORFik, OrganismDbi, OUTRIDER, proActiv, proBAMr, QuasR, RCAS, recoup, Rhisat2, RiboDiPA, ribosomeProfilingQC, RNAmodR, scanMiRApp, scruff, sitadela, trackViewer, txcutr, tximeta, geneLenDataBase
Suggests Me AnnotationHub, bumphunter, BUSpaRse, DEXSeq, doubletrouble, eisaR, FLAMES, GenomicFeatures, GenomicRanges, 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.

Source Package txdbmaker_1.0.0.tar.gz
Windows Binary txdbmaker_1.0.0.zip
macOS Binary (x86_64) txdbmaker_1.0.0.tgz
macOS Binary (arm64) txdbmaker_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/txdbmaker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/txdbmaker
Bioc Package Browser https://code.bioconductor.org/browse/txdbmaker/
Package Short Url https://bioconductor.org/packages/txdbmaker/
Package Downloads Report Download Stats