abseqR: reporting functions and downstream analysis of antibody libraries Rep-Seq

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 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.

Note that abseqR does not require abseqPy to be installed to work but the output of abseqPy must be already present to invoke abseqR's functions.

Developers

• AbSeq is developed by JiaHong Fong and Monther Alhamdoosh

• For comments and suggestions, email jiahfong <at> gmail <dot> com

Installation

System requirements

pandoc is highly recommended. If abseqR fails to detect pandoc in your system's PATH variable, it will not be able to generate a collated HTML report yet you can still access individual plots.

Make sure pandoc is at least version 1.19.2.1

Installation

Install from Bioconductor

As soon as abseqR is available in the Bioconductor project, it can be installed from R console as follows:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("abseqR")

Install from GitHub

To install the development version of abseqR from GitHub, type the following commands in R Console:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("malhamdoosh/abseqR")

Quick start

Assuming abseqPy has completed an analysis and the output directory was named output, a basic usage of abseqR is:

library(abseqR)
abseqReport("/path/to/output")

This will generate an interctive report of the analysis results. Please refer to the package's main vignette for more advanced use cases.

Features

abseqR generates numerous plots for the quality control analysis of antibody libraries and collates the results into an interactive HTML report.

Additional plots along with documentation can be found in abseqR's main vignette.

In R console, type:

browseVignettes("abseqR")