EpiTxDb

This is the released version of EpiTxDb; for the devel version, see EpiTxDb.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Bioconductor version: Release (3.23)

EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.

Author: Felix G.M. Ernst [aut, cre] ORCID: 0000-0001-5064-0928

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

Citation (from within R, enter citation("EpiTxDb")):

Felix G.M. Ernst. EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface. doi:10.18129/B9.bioc.EpiTxDb, R package version 1.24.0, https://bioconductor.org/packages/EpiTxDb.

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")

BiocManager::install("EpiTxDb")

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("EpiTxDb")

EpiTxDb-creation	HTML	R Script
EpiTxDb	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Epitranscriptomics, Software
Version	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), AnnotationDbi, Modstrings
Imports	methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, Seqinfo, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport
System Requirements
URL	https://github.com/FelixErnst/EpiTxDb
Bug Reports	https://github.com/FelixErnst/EpiTxDb/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene
Linking To
Enhances
Depends On Me	EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	EpiTxDb_1.24.0.tar.gz
Windows Binary (x86_64)	EpiTxDb_1.24.0.zip
macOS Binary (big-sur-x86_64)	EpiTxDb_1.24.0.tgz
macOS Binary (sonoma-arm64)	EpiTxDb_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EpiTxDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EpiTxDb
Package Short Url	https://bioconductor.org/packages/EpiTxDb/
Package Downloads Report	Download Stats