PhIPData

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

Container for PhIP-Seq Experiments

Bioconductor version: 3.19

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>

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

Installation

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

PhIPData: A Container for PhIP-Seq Experiments HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataRepresentation, Infrastructure, Sequencing, Software

Version 1.12.0

In Bioconductor since BioC 3.13 (R-4.1) (3.5 years)

License MIT + file LICENSE

Depends R (>= 4.1.0), SummarizedExperiment(>= 1.3.81)

Imports BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils

System Requirements

URL

Bug Reports https://github.com/athchen/PhIPData/issues

Suggests BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr

Linking To

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Package Archives

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

Source Package PhIPData_1.12.0.tar.gz

Windows Binary (x86_64) PhIPData_1.12.0.zip

macOS Binary (x86_64) PhIPData_1.12.0.tgz

macOS Binary (arm64) PhIPData_1.12.0.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/

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