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Bioconductor - tripr (development version)

tripr

This is the development version of tripr; for the stable release version, see tripr.

T-cell Receptor/Immunoglobulin Profiler (TRIP)

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Details biocViews BatchEffect, GeneExpression, ImmunoOncology, MultipleComparison, Software, TargetedResequencing Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License MIT + file LICENSE Depends R (>= 4.1.0), 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, vegan 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 Build Report Build Report Package Archives

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

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