PhIPData

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

Container for PhIP-Seq Experiments


Bioconductor version: Development (3.20)

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")

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

Details

biocViews Coverage, DataRepresentation, Infrastructure, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
Suggests BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr
Linking To
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Depends On Me beer
Imports Me
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Package Archives

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

Source Package PhIPData_1.13.0.tar.gz
Windows Binary PhIPData_1.13.0.zip
macOS Binary (x86_64) PhIPData_1.13.0.tgz
macOS Binary (arm64) PhIPData_1.13.0.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