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
plotting and reporting capabilities and
allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally,
abseqPy to compare multiple
repertoire analyses and perform further downstream analysis on its output.
abseqR does not require
abseqPy to be installed to work but the output of
abseqPy must be already present to invoke
AbSeq is developed by JiaHong Fong and Monther Alhamdoosh
For comments and suggestions, email jiahfong \<at> gmail \<dot> com
pandoc is highly
abseqR fails to detect
pandoc in your
PATH variable, it will not be able to generate a collated HTML report yet you can still access individual plots.
pandocis at least version 126.96.36.199
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")
To install the development version of
from GitHub, type the following commands in R Console:
if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("malhamdoosh/abseqR")
abseqPy has completed an analysis and the output directory was
output, a basic usage of
This will generate an interctive report of the analysis results. Please refer to the package's main vignette for more advanced use cases.
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:
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