Tag: tcR

CATT 1.9 – CharActerzing TCR Repertoires

CATT 1.9

:: DESCRIPTION

CATT is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq, scRNA-seq and any TCR contained sequencing data).

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Julia

:: DOWNLOAD

CATT

:: MORE INFORMATION

Citation

Chen SY, Liu CJ, Zhang Q, Guo AY.
An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data.
Bioinformatics. 2020 Aug 1;36(15):4255-4262. doi: 10.1093/bioinformatics/btaa432. PMID: 32399561.

PAComplex – Infer Peptide Antigen Family and TCR-pMHC Binding Model

PAComplex

:: DESCRIPTION

PAComplex is a web server investigating and visualizing both TCR-peptide / peptide-MHC interfaces; furthermore, it provides biological insights of TCR-pMHC binding models.

::DEVELOPER

PAComplex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W254-60. doi: 10.1093/nar/gkr434. Epub 2011 Jun 11.
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.
Liu IH1, Lo YS, Yang JM.

LymAnalyzer 1.2.2 – Analysis TCR/IG Repertoire from High-throughput Sequencing reads

LymAnalyzer 1.2.2

:: DESCRIPTION

LymAnalyzer is a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.

::DEVELOPER

LymAnalyzer team

:: SCREENSHOTS

lymanalyzer

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 LymAnalyzer

:: MORE INFORMATION

Citation:

LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.
Yu Y, Ceredig R, Seoighe C.
Nucleic Acids Res. 2015 Oct 7. pii: gkv1016.

TRUST4 v0.1.1 – TCR and BCR Assembly from RNA-seq data

TRUST4 v0.1.1

:: DESCRIPTION

TRUST (T cell receptor Repertoire Utilities for Solid Tissue/Tumor) is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRUST

:: MORE INFORMATION

 

tcR 2.2.4 – T Cell Receptor Repertoire Advanced data analysis

tcR 2.2.4

:: DESCRIPTION

tcR is a platform designed for TCR repertoire data analysis in R after preprocessing data with CDR3 extraction and gene alignment software tools such as MiTCR, ImmunoSEQ and MiGEC.

::DEVELOPER

Laboratory of Comparative and Functional Genomic

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

 tcR

:: MORE INFORMATION

Citation:

tcR: an R package for T cell receptor repertoire advanced data analysis.
Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ.
BMC Bioinformatics. 2015 May 28;16:175. doi: 10.1186/s12859-015-0613-1.