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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 (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews MultipleComparison, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (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
Linking To
Suggests testthat
System Requirements pandoc (>= 1.19.2.1)
Enhances
URL https://github.com/malhamdoosh/abseqR
Bug Reports https://github.com/malhamdoosh/abseqR/issues
See More
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package abseqR_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64) abseqR_1.19.0.tgz
macOS Binary (arm64) abseqR_1.19.0.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