IgIDivA (Immunoglobulin Intraclonal Diversification Analysis) is a purpose-built tool for the analysis of the intraclonal diversification process using high-throughput sequencing data. It is written in shiny. Every step of the analysis can be performed interactively, thus not requiring any programming skills. It takes as input the output files "clonotypes_computation" and "grouped_alignment_nt" from the tripr package.
Functions for an R command-line use are also available.
The UserGuide of IgIDivA can be found here and an example dataset to be used as Input of IgIDivA can be found here.
The IgIDivA scripts can be freely downloaded here.
It requires R (version "4.1"), which can be installed on any operating system from CRAN. IgIDivA has been successfully tested in Windows 10, macOS 10.15 and Linux WSL.
All the packages that need to be installed in your R session are the following:
install.packages("shiny")
install.packages("shinyFiles")
install.packages("fs")
install.packages("pdftools")
install.packages("purrr")
install.packages("DT")
install.packages("bslib")
install.packages("shinyhelper")
install.packages("data.table")
install.packages("stringr")
install.packages("RGenetics")
install.packages("dplyr")
install.packages("ggsci")
install.packages("tidygraph")
install.packages("ggraph")
install.packages("igraph")
install.packages("ggplot2")
install.packages("ggpubr")
install.packages("rstatix")
install.packages("shinyvalidate")
All the scripts need to be downloaded in the same folder, and the input should be saved in a folder called Input
To run the app, open the script app.R in your R session and press the button Run App.
Alternatively, IgIDivA can be installed using a conda environment. We recommend to use Miniconda to install all the dependencies. The dependencies can be found in .yml format in the IgIDivA GitHub repository. The yml file and the IgIDivA scripts need to be stored in the working folder. After downloading all the files, a terminal should be opened and the following commands should be written:
conda env create -f IgIDivA.yml
conda activate IgIDivA
R
install.packages(c("shinyvalidate", "RGenetics","rstatix"))
q()
Rscript app.RThis will produce a url that can be copied in a web browser and will direct the user to the IgIDivA app.