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Bioconductor - PhIPData (development version)

PhIPData

This is the development version of PhIPData; for the stable release version, see PhIPData.

Container for PhIP-Seq Experiments

Bioconductor version: Development (3.22)

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] ORCID: 0000-0001-6900-2264 , 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Coverage, DataRepresentation, Infrastructure, Sequencing, Software Version 1.17.0 In Bioconductor since BioC 3.13 (R-4.1) (4 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 See More Package Archives

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

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