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>
citation("tripr")):
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")| tripr User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, GeneExpression, ImmunoOncology, MultipleComparison, Software, TargetedResequencing |
| Version | 1.0.0 |
| 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, pryr, 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 |
| 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.
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/tripr/ |
| Package Short Url | https://bioconductor.org/packages/tripr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |