PhIPData
This is the released version of PhIPData; for the devel version, see PhIPData.
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]
, Rob Scharpf [aut], Ingo Ruczinski [aut]
Maintainer: Athena Chen <achen70 at jhu.edu>
citation("PhIPData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataRepresentation, Infrastructure, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.20.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/PhIPData/ |
| Package Short Url | https://bioconductor.org/packages/PhIPData/ |
| Package Downloads Report | Download Stats |