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tripr

T-cell Receptor/Immunoglobulin Profiler (TRIP)


Bioconductor version: Release (3.18)

TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.

Author: Maria Th. Kotouza [aut], Katerina Gemenetzi [aut], Chrysi Galigalidou [aut], Elisavet Vlachonikola [aut], Nikolaos Pechlivanis [cre], Andreas Agathangelidis [aut], Raphael Sandaltzopoulos [aut], Pericles A. Mitkas [aut], Kostas Stamatopoulos [aut], Anastasia Chatzidimitriou [aut], Fotis E. Psomopoulos [aut], Iason Ofeidis [aut], Aspasia Orfanou [aut]

Maintainer: Nikolaos Pechlivanis <inab.bioinformatics at lists.certh.gr>

Citation (from within R, enter citation("tripr")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tripr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tripr")
tripr User Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BatchEffect, GeneExpression, ImmunoOncology, MultipleComparison, Software, TargetedResequencing
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends shiny (>= 1.6.0), shinyBS
Imports shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils
System Requirements
URL https://github.com/BiodataAnalysisGroup/tripr
Bug Reports https://github.com/BiodataAnalysisGroup/tripr/issues
See More
Suggests BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr
Linking To
Enhances parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tripr_1.8.0.tar.gz
Windows Binary tripr_1.8.0.zip
macOS Binary (x86_64) tripr_1.8.0.tgz
macOS Binary (arm64) tripr_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tripr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tripr
Bioc Package Browser https://code.bioconductor.org/browse/tripr/
Package Short Url https://bioconductor.org/packages/tripr/
Package Downloads Report Download Stats