txdbmaker

Tools for making TxDb objects from genomic annotations

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

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

BiocManager::install("txdbmaker")

Details

Maintainer	H. Pagès <hpages.on.github@gmail.com>
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]
License	Artistic-2.0
URL	https://bioconductor.org/packages/txdbmaker
Bug Reports	https://github.com/Bioconductor/txdbmaker/issues
Downloads rank	5765
Source branch	RELEASE_3_23
biocViews	Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software

Documentation

Making TxDb Objects

Download

Source package

Dependencies

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)

Suggests: RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle, knitr

Reverse dependencies

Depends On Me (1): mygene

Imports Me (39): APAlyzer, ASpli, BgeeCall, casper, crisprDesign, crisprViz, customProDB, DegNorm, DOTSeq, ELViS, EpiTxDb, EventPointer, ExpHunterSuite, FRASER, geneLenDataBase, GenomicPlot, GenomicState, IntEREst, metaseqR2, ORFik, OUTRIDER, proActiv, proBAMr, profileplyr, QuasR, RCAS, recoup, Rhisat2, RiboDiPA, ribosomeProfilingQC, RNAmodR, scafari, scanMiRApp, scruff, sitadela, trackViewer, txcutr, tximeta, wavClusteR

Suggests Me (19): AnnotationHub, BindingSiteFinder, Bioc.gff, bumphunter, BUSpaRse, DEXSeq, doubletrouble, eisaR, GenomicFeatures, GenomicRanges, OrganismDbi, polyRAD, raer, recount, saseR, SplicingGraphs, SPLINTER, systemPipeR, systemPipeRdata