tripr

DOI: 10.18129/B9.bioc.tripr    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see tripr.

T-cell Receptor/Immunoglobulin Profiler (TRIP)

Bioconductor version: 3.14

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 [aut], Andreas Agathangelidis [aut], Raphael Sandaltzopoulos [aut], Pericles A. Mitkas [aut], Kostas Stamatopoulos [aut], Anastasia Chatzidimitriou [aut], Fotis E. Psomopoulos [aut], Iason Ofeidis [cre]

Maintainer: Iason Ofeidis <jasonof at certh.gr>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	tripr User Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BatchEffect, GeneExpression, ImmunoOncology, MultipleComparison, Software, TargetedResequencing
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	shiny (>= 1.6.0), shinyBS
Imports	shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, pryr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils
LinkingTo
Suggests	BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis
SystemRequirements
Enhances	parallel
URL	https://github.com/BiodataAnalysisGroup/tripr
BugReports	https://github.com/BiodataAnalysisGroup/tripr/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	tripr_1.0.0.tar.gz
Windows Binary	tripr_1.0.0.zip
macOS 10.13 (High Sierra)	tripr_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tripr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tripr
Package Short Url	https://bioconductor.org/packages/tripr/
Package Downloads Report	Download Stats