EpiTxDb

DOI: 10.18129/B9.bioc.EpiTxDb    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see EpiTxDb.

Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Bioconductor version: 3.15

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]

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

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Epitranscriptomics, Software
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), AnnotationDbi, Modstrings
Imports	methods, utils, httr, xml2, curl, GenomicFeatures, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/FelixErnst/EpiTxDb
BugReports	https://github.com/FelixErnst/EpiTxDb/issues
Depends On Me	EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	EpiTxDb_1.8.0.tar.gz
Windows Binary	EpiTxDb_1.8.0.zip
macOS Binary (x86_64)	EpiTxDb_1.8.0.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