PhIPData

This is the released version of PhIPData; for the devel version, see PhIPData.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Container for PhIP-Seq Experiments

Bioconductor version: Release (3.23)

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")):

Athena Chen, Rob Scharpf, Ingo Ruczinski. PhIPData: Container for PhIP-Seq Experiments. doi:10.18129/B9.bioc.PhIPData, R package version 1.20.0, https://bioconductor.org/packages/PhIPData.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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
Enhances
Depends On Me	beer
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PhIPData_1.20.0.tar.gz
Windows Binary (x86_64)	PhIPData_1.20.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	PhIPData_1.20.0.tgz
macOS Binary (sonoma-arm64)	PhIPData_1.20.0.tgz
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