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("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 | ||
| 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 |