PhIPData

DOI: 10.18129/B9.bioc.PhIPData  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see PhIPData.

Container for PhIP-Seq Experiments

Bioconductor version: 3.16

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

Author: Athena Chen [aut, cre] , Rob Scharpf [aut], Ingo Ruczinski [aut]

Maintainer: Athena Chen <achen70 at jhu.edu>

Installation

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

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

BiocManager::install("PhIPData")

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("PhIPData")

 

HTML	R Script	PhIPData: A Container for PhIP-Seq Experiments
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, DataRepresentation, Infrastructure, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), SummarizedExperiment(>= 1.3.81)
Imports	BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr
SystemRequirements
Enhances
URL
BugReports	https://github.com/athchen/PhIPData/issues
Depends On Me	beer
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PhIPData_1.6.0.tar.gz
Windows Binary	PhIPData_1.6.0.zip
macOS Binary (x86_64)	PhIPData_1.6.0.tgz
macOS Binary (arm64)	PhIPData_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PhIPData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PhIPData
Bioc Package Browser	https://code.bioconductor.org/browse/PhIPData/
Package Short Url	https://bioconductor.org/packages/PhIPData/
Package Downloads Report	Download Stats