EpiTxDb

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see EpiTxDb.

Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Epitranscriptomics, Software

Version 1.16.0

In Bioconductor since BioC 3.11 (R-4.0) (4.5 years)

License Artistic-2.0

Depends R (>= 4.0), AnnotationDbi, Modstrings

Imports methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, 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

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_1.16.0.tar.gz

Windows Binary (x86_64) EpiTxDb_1.16.0.zip

macOS Binary (x86_64) EpiTxDb_1.16.0.tgz

macOS Binary (arm64) EpiTxDb_1.16.0.tgz

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/

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