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EpiTxDb

This is the development version of EpiTxDb; for the stable release version, see EpiTxDb.

Storing and accessing epitranscriptomic information using the AnnotationDbi interface


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Epitranscriptomics, Software
Version 1.15.1
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL https://github.com/FelixErnst/EpiTxDb
Bug Reports https://github.com/FelixErnst/EpiTxDb/issues
See More
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

Package Archives

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

Source Package EpiTxDb_1.15.1.tar.gz
Windows Binary EpiTxDb_1.15.1.zip (64-bit only)
macOS Binary (x86_64) EpiTxDb_1.15.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/EpiTxDb
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EpiTxDb
Bioc Package Browser https://code.bioconductor.org/browse/EpiTxDb/
Package Short Url https://bioconductor.org/packages/EpiTxDb/
Package Downloads Report Download Stats