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 | 5805 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataImport, Genetics, GenomeAnnotation, GenomeAssembly, Infrastructure, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | txdbmaker_1.8.0.tar.gz |
| Windows binary (x86_64) | txdbmaker_1.8.0.zip |
| macOS binary (arm64) | txdbmaker_1.7.3.tgz |
| macOS binary (x86_64) | txdbmaker_1.7.3.tgz |
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