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# 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 ### Installation #### Install from Bioconductor As soon as `abseqR` is available in the [Bioconductor]( project, it can be installed from R console as follows: ```r 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: ```r 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: ```r 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. <div align="center"> <img src="man/figures/abseq_gif.gif" width=791 height=474> </div> Additional plots along with documentation can be found in `abseqR`'s main vignette. In R console, type: ```r browseVignettes("abseqR") ```