PhIPData

DOI: 10.18129/B9.bioc.PhIPData    

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

Container for PhIP-Seq Experiments

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Coverage, DataRepresentation, Infrastructure, Sequencing, Software
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.1.0), SummarizedExperiment(>= 1.3.81)
Imports 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
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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/PhIPData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PhIPData
Package Short Url https://bioconductor.org/packages/PhIPData/
Package Downloads Report Download Stats

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