PhIPData

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see PhIPData.

Container for PhIP-Seq Experiments


Bioconductor version: 3.13

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 "4.1") 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

Details

biocViews Coverage, DataRepresentation, Infrastructure, Sequencing, Software
Version 1.0.0
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 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package PhIPData_1.0.0.tar.gz
Windows Binary PhIPData_1.0.0.zip
macOS 10.13 (High Sierra) PhIPData_1.0.0.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
Old Source Packages for BioC 3.13 Source Archive