Other packages > Find by keyword >

ClusTCR2  

Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'
View on CRAN: Click here


Download and install ClusTCR2 package within the R console
Install from CRAN:
install.packages("ClusTCR2")

Install from Github:
library("remotes")
install_github("cran/ClusTCR2")

Install by package version:
library("remotes")
install_version("ClusTCR2", "1.7.3.01")



Attach the package and use:
library("ClusTCR2")
Maintained by
Kerry A. Mullan
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2024-05-16
Latest Update: 2024-05-16
Description:
Enhancing T cell receptor (TCR) sequence analysis, 'ClusTCR2', based on 'ClusTCR' python program, leverages Hamming distance to compare the complement-determining region three (CDR3) sequences for sequence similarity, variable gene (V gene) and length. The second step employs the Markov Cluster Algorithm to identify clusters within an undirected graph, providing a summary of amino acid motifs and matrix for generating network plots. Tailored for single-cell RNA-seq data with integrated TCR-seq information, 'ClusTCR2' is integrated into the Single Cell TCR and Expression Grouped Ontologies (STEGO) R application or 'STEGO.R'. See the two publications for more details. Sebastiaan Valkiers, Max Van Houcke, Kris Laukens, Pieter Meysman (2021) <doi:10.1093/bioinformatics/btab446>, Kerry A. Mullan, My Ha, Sebastiaan Valkiers, Nicky de Vrij, Benson Ogunjimi, Kris Laukens, Pieter Meysman (2023) <doi:10.1101/2023.09.27.559702>.
How to cite:
Kerry A. Mullan (2024). ClusTCR2: Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'. R package version 1.7.3.01, https://cran.r-project.org/web/packages/ClusTCR2. Accessed 16 Jul. 2026.
Previous versions and publish date:
No previous versions
Other packages that cited ClusTCR2 R package
View ClusTCR2 citation profile
Other R packages that ClusTCR2 depends, imports, suggests or enhances
Complete documentation for ClusTCR2
Functions, R codes and Examples using the ClusTCR2 R package
Full ClusTCR2 package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

Rnmr1D  
Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free ...
Download / Learn more Package Citations See dependency  
schoolmath  
Functions and Datasets for Math Used in School
Contains functions and datasets for math taught in school. A main focus is set to prime-calculation. ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
stevedata  
Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
This is a collection of various kinds of data with broad uses for teaching. My students, and academ ...
Download / Learn more Package Citations See dependency  
tibble  
Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the tradi ...
Download / Learn more Package Citations See dependency  
wordnet  
WordNet Interface
An interface to WordNet using the Jawbone Java API to WordNet. WordNet (< ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA