High throughput sequencing of immune cell receptor sequences presents a unique opportunity to inform our understanding of immunological response to infection and how we can detect it. iCAT is a user-friendly, graphical-interface software that takes exposed and non-exposed samples of T-cell receptor (TCR) clonotypes as input and identifies pathogen-specific TCR sequences. Using these sequences, iCAT can also classify independent samples of TCR clonotypes. iCAT was able to identify vaccine-accosiated TCR seqeunces with up to 95% accuracy in mice.


Pre-requisites:

To install devtools, use the command:

install.packages("devtools") 

Note: iCAT also uses shiny, shinyjs, data.table, ggplot2, DT, hash, and magrittr. However, those packages will be installed if using install_github from below.

Installing iCAT

Using an R interface, type:

devtools::install_github("BioHPC/iCAT")