Publication details
tcR: an R package for T cell receptor repertoire advanced data analysis
| Authors | |
|---|---|
| Year of publication | 2015 |
| Type | Article in Periodical |
| Magazine / Source | BMC Bioinformatics |
| MU Faculty or unit | |
| Citation | |
| web | http://download.springer.com/static/pdf/403/art%253A10.1186%252Fs12859-015-0613-1.pdf?originUrl=http%3A%2F%2Fbmcbioinformatics.biomedcentral.com%2Farticle%2F10.1186%2Fs12859-015-0613-1&token2=exp=1452494593~acl=%2Fstatic%2Fpdf%2F403%2Fart%25253A10.1186%2 |
| Doi | http://dx.doi.org/10.1186/s12859-015-0613-1 |
| Field | Biochemistry |
| Keywords | Adaptive immunity; T cell receptor; TR repertoire analysis; TR diversity |
| Description | Background The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. Results Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies. Conclusions tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html webcite). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/ webcite) along with the full documentation and typical usage examples. |