T-cell repertoire annotation and motif discovery tutorial

This tutorial provides a basic introduction to the inference of T-cells specific to certain epitopes and T-cell receptor sequence motif extraction from high-throughput sequencing data (RepSeq). The users will get familiar with VDJdb and VDJtools software and learn some tricks for working with TCR sequences and TCR sequence motifs in R.

Prerequisites

The following software is required to run the tutorial:

• Java v1.10 Can be downloaded from Java SE Runtime Environment 10 Downloads or installed by other means.

• RStudio Can be installed from rstudio.com.

• R packages Run the following command in RStudio:

install.packages(c(
	"dplyr", "data.table", "ggplot2",
	"forcats", "parallel", "stringr",
	"reshape2", "igraph", "msa",
	"stringdist", "broom", "GGally",
	"ggseqlogo", "network", "gridExtra",
	"cowplot"
	)
)

or install these packages manually.

Download the tutorial by clicking the Clone or download button above or executing

git clone https://github.com/antigenomics/sciar-tutorial-2018.git

Then open the R markdown template tutorial.Rmd in RStudio and proceed with executing the R code. For more information on R markdown please visit the following link.

Materials

• The slides can be found in slides/slides.pdf. For the interactive part open the tutorial.Rmd file in RStudio.

• The compiled tutorial results are stored in the tutorial.pdf, this file contains the code, comments and plots.

• Additional files and scripts for tracking expansion of CMV+ clonotypes post HSCT treatment are provided in the extra/ folder