PhIPData
This is the development version of PhIPData; for the stable release version, see PhIPData.
Container for PhIP-Seq Experiments
Bioconductor version: Development (3.20)
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 "4.4") and enter:
if (!require("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")
PhIPData: A Container for PhIP-Seq Experiments | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Coverage, DataRepresentation, Infrastructure, Sequencing, Software |
Version | 1.13.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
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 |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | PhIPData_1.13.0.tar.gz |
Windows Binary | PhIPData_1.13.0.zip |
macOS Binary (x86_64) | PhIPData_1.13.0.tgz |
macOS Binary (arm64) | PhIPData_1.13.0.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 |