abseqR

DOI: 10.18129/B9.bioc.abseqR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see abseqR.

Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Bioconductor version: 3.16

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

Author: JiaHong Fong [cre, aut], Monther Alhamdoosh [aut]

Maintainer: JiaHong Fong <jiahfong at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("abseqR")

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("abseqR")

 

PDF	R Script	Introduction to abseqR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	MultipleComparison, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	GPL-3 | file LICENSE
Depends	R (>= 3.5.0)
Imports	ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel(>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics
LinkingTo
Suggests	testthat
SystemRequirements	pandoc (>= 1.19.2.1)
Enhances
URL	https://github.com/malhamdoosh/abseqR
BugReports	https://github.com/malhamdoosh/abseqR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	abseqR_1.16.0.tar.gz
Windows Binary	abseqR_1.16.0.zip
macOS Binary (x86_64)	abseqR_1.16.0.tgz
macOS Binary (arm64)	abseqR_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/abseqR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/abseqR
Bioc Package Browser	https://code.bioconductor.org/browse/abseqR/
Package Short Url	https://bioconductor.org/packages/abseqR/
Package Downloads Report	Download Stats