abseqR

DOI: 10.18129/B9.bioc.abseqR    

This is the development version of abseqR; for the stable release version, see abseqR.

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

Bioconductor version: Development (3.9)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("abseqR", version = "3.9")

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 1.1.0
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_1.1.0.tar.gz
Windows Binary abseqR_1.1.0.zip
Mac OS X 10.11 (El Capitan) abseqR_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/abseqR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/abseqR
Package Short Url http://bioconductor.org/packages/abseqR/
Package Downloads Report Download Stats

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