index.md

In jonathan-mcmillan/csci3500: immune Cell Analysis Tool

Immune Cells Analysis software Tool

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:

• R version

• Download R (>3.4.0) version from CRAN.

  • Windows: https://cran.r-project.org/bin/windows/base/
  • Mac OS X: https://cran.r-project.org/bin/macosx/
  • Linux: https://cran.r-project.org/bin/linux/

• Libraries:

  • devtools

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") 

jonathan-mcmillan/csci3500 documentation built on Jan. 31, 2020, 12:25 a.m.