Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

CCBYSA

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.

Splash

Prerequisites

The following software is required to run the tutorial:

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

About

πŸ“ [Paper/Tutorial] T-cell repertoire annotation and motif discovery

Resources

License

Releases

No releases published

Packages

No packages published

Languages