abseqR
This is the released version of abseqR; for the devel version, see abseqR.
All Bioconductor versions of abseqR
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Bioconductor version: 3.23 · Package version: 1.30.0
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"):
JiaHong Fong, Monther Alhamdoosh. abseqR: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries. doi:10.18129/B9.bioc.abseqR, R package version 1.30.0, https://bioconductor.org/packages/abseqR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.30.0 |
| License | GPL-3 | file LICENSE |
| URL | https://github.com/malhamdoosh/abseqR |
| Bug Reports | https://github.com/malhamdoosh/abseqR/issues |
| System Requirements | pandoc (>= 1.19.2.1) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 1266 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | MultipleComparison, QualityControl, ReportWriting, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/abseqR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("abseqR")| abseqR: reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | abseqR_1.30.0.tar.gz |
| Windows binary (x86_64) | abseqR_1.30.0.zip |
| macOS binary (arm64) | abseqR_1.30.0.tgz |
| macOS binary (x86_64) | abseqR_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/abseqR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/abseqR |
| Package Downloads Report | Download Stats |
Dependencies
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
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