tripr
This is the released version of tripr; for the devel version, see tripr.
T-cell Receptor/Immunoglobulin Profiler (TRIP)
Bioconductor version: Release (3.23)
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("tripr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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 |
| 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | tripr_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | tripr_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | tripr_1.18.0.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 |