Advanced Data Analysis of Immune Receptor Repertoires

Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.


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The package is no longer supported. If you would like to help us understand how we can improve the quality of your research and what features we should add that suit your needs, please complete a survey on immune repertoire analysis and help us understand what features should we definitely implement. Link to the survey: https://goo.gl/forms/RcLqJwkUPNfKfaOw2

tcR is a platform designed for TCR and Ig repertoire data analysis in R after preprocessing data with software tools for CDR3 extraction and gene segments aligning (MiTCR, MiXCR, MiGEC, ImmunoSEQ, IMSEQ, etc.). With the power and flexibility of R language and procedures supported by tcR users can perform advanced statistical analysis of TCR and Ig repertoires. The package was published in BMC Bioinformatics, please cite if you use it:

Nazarov et al., tcR: an R package for T cell receptor repertoire advanced data analysis

See tcR website for more information, manual and examples: http://imminfo.github.io/tcr/

If you have any questions, suggestions or bug reports, feel free to raise an issue here: https://github.com/imminfo/tcr/issues

The project was developed mainly in the Laboratory of Comparative and Functional Genomics.

Warning! tcR internally expects columns with nucleotide and amino acid CDR3 sequences and columns with gene segments to have character class, not factor class. Use stringsAsFactors=FALSE parameter if you use R functions for parsing files with tables (.csv, .xls and others).

Note for installation on Macs with OSX Yosemite (and potentially other versions): if you receive a compilation error, modify tcR/src/Makvars to:

CXX=clang++

News

VERSION 1.3

Reference manual

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install.packages("tcR")

2.2.4 by Vadim Nazarov, 9 months ago


http://imminfo.github.io/tcr/


Report a bug at https://github.com/imminfo/tcr/issues


Browse source code at https://github.com/cran/tcR


Authors: Vadim Nazarov


Documentation:   PDF Manual  


Apache License 2.0 license


Imports utils, Rcpp, grid, data.table, gtable, stringdist, scales

Depends on ggplot2, dplyr, gridExtra, reshape2, igraph

Suggests knitr, roxygen2, rmarkdown

Linking to Rcpp


Imported by kmeRs.


See at CRAN