EuPathDB
This is the released version of EuPathDB; for the devel version, see EuPathDB.
Provides access to pathogen annotation resources available on EuPathDB databases
Bioconductor version: Release (3.23)
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("EuPathDB")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
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 |
See More
| Suggests | dplyr, knitr, BiocStyle, rmarkdown, jsonlite |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EuPathDB_1.0.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/EuPathDB/ |
| Package Downloads Report | Download Stats |