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>
citation("abseqR")):
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")| Introduction to abseqR | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MultipleComparison, QualityControl, ReportWriting, Sequencing, Software, Visualization |
| Version | 1.16.0 |
| 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 |
See More
| 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_1.16.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |