PhIPData
This is the released version of PhIPData; for the devel version, see PhIPData.
All Bioconductor versions of PhIPData
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: 3.23 · Package version: 1.20.0
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"):
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.
Details
| Version | 1.20.0 |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/athchen/PhIPData/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| Downloads rank | 1487 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, DataRepresentation, Infrastructure, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/PhIPData/ |
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 | ||
| NEWS | Text |
Download
Follow the 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 |
| macOS binary (arm64) | PhIPData_1.20.0.tgz |
| macOS binary (x86_64) | 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 Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils
Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr
Reverse dependencies
Depends On Me (1): beer