abseqR

This package is for version 3.10 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: 3.10

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>

Citation (from within R, enter citation("abseqR")):

Installation

To install this package, start R (version "3.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MultipleComparison, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.8 (R-3.5) (5.5 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
System Requirements	pandoc (>= 1.19.2.1)
URL	https://github.com/malhamdoosh/abseqR
Bug Reports	https://github.com/malhamdoosh/abseqR/issues

Suggests	testthat
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	abseqR_1.4.0.tar.gz
Windows Binary	abseqR_1.4.0.zip
Mac OS X 10.11 (El Capitan)	abseqR_1.4.0.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
Old Source Packages for BioC 3.10	Source Archive