EuPathDB

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see EuPathDB.

Provides access to pathogen annotation resources available on EuPathDB databases

Bioconductor version: 3.17

Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.

Author: Keith Hughitt [aut, cre]

Maintainer: Keith Hughitt <keith.hughitt at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


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

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("EuPathDB")

Accessing EuPathDB Resources using AnnotationHub HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AnnotationData, AnnotationHub, DataImport, EuPathDB

Version 1.0.1

License Artistic-2.0

Depends R (>= 3.5), Biobase, GenomicRanges, GenomeInfoDbData, AnnotationHub(>= 2.13.8)

Imports AnnotationHubData, Biostrings, BiocManager, utils

System Requirements

URL https://github.com/khughitt/EuPathDB

Bug Reports https://github.com/khughitt/EuPathDB/issues

Suggests dplyr, knitr, BiocStyle, rmarkdown, jsonlite

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Package Archives

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

Source Package EuPathDB_1.0.1.tar.gz

Windows Binary

macOS Binary (x86_64)

macOS Binary (arm64)

Package Short Url https://bioconductor.org/packages/EuPathDB/

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