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tripr

T-cell Receptor/Immunoglobulin Profiler {tripr}

https://github.com/iofeidis/tripr

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

T-cell Receptor/Immunoglobulin Profiler {tripr}

Basic Info
  • Host: GitHub
  • Owner: iofeidis
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 9.96 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed over 4 years ago
Metadata Files
Readme Changelog License Citation

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```






# tripr 

T-cell Receptor/Immunoglobulin Profiler (TRIP)

## Description

`tripr` is a [Bioconductor](http://bioconductor.org) package,
written in [shiny](https://shiny.rstudio.com/) that provides
analytics services on 
antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, 
TR) gene sequence data. Every step of the analysis can be
performed interactively, thus not requiring any programming skills. It takes
as input the output files of the 
[IMGT/HighV-Quest tool](http://www.imgt.org/HighV-QUEST/home.action). 
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. 

Functions for an `R` command-line use are also available.

## Installation





To install `tripr` from github use:

```{r eval=FALSE}
remotes::install_github("iofeidis/tripr", dependencies = TRUE)
```

## Launching the app

Once `tripr` is successfully installed, it can be loaded as follow:

```{r eval=FALSE}
library(tripr)
```

## User Guide

Have a look at our thorough `tripr` user guide (on 
[*dev* branch](https://github.com/iofeidis/tripr/tree/dev)) with:


```{r eval=FALSE}
browseURL(url = "vignettes/tripr_guide.html") 
```

Owner

  • Name: Iason Ofeidis
  • Login: iofeidis
  • Kind: user
  • Location: New Haven, US
  • Company: Yale University

Citation (CITATION.cff) 

# YAML 1.2
---
authors: 
  -
    family-names: Kotouza
    given-names: "Maria Th."
    orcid: "https://orcid.org/0000-0002-5375-5410"
  -
    family-names: Gemenetzi
    given-names: Katerina
    orcid: "https://orcid.org/0000-0002-0216-0257"
  -
    family-names: Galigalidou
    given-names: Chrysi
  -
    family-names: Vlachonikola
    given-names: Elisavet
    orcid: "https://orcid.org/0000-0003-4609-9977"
  -
    family-names: Pechlivanis
    given-names: Nikolaos
    orcid: "https://orcid.org/0000-0003-2502-612X"
  -
    family-names: Agathangelidis
    given-names: Andreas
    orcid: "https://orcid.org/0000-0002-8467-7945"
  -
    family-names: Sandaltzopoulos
    given-names: Raphael
    orcid: "https://orcid.org/0000-0002-8490-4300"
  -
    family-names: Mitkas
    given-names: "Pericles A."
  -
    family-names: Stamatopoulos
    given-names: Kostas
  -
    family-names: Chatzidimitriou
    given-names: Anastasia
  -
    family-names: Psomopoulos
    given-names: "Fotis E."
    orcid: "https://orcid.org/0000-0002-0222-4273"
  
  
cff-version: "1.1.0"
date-released: 2020-09-29
doi: "10.1186/s12859-020-03669-1"
keywords: 
  - "Antigen receptor"
  - "Software pipeline"
  - "R shiny"
license: MIT
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/BiodataAnalysisGroup/TRIP"
title: "T-cell Receptor/Immunoglobulin Profiler (TRIP)"
version: "0.99.0"
...

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Dependencies

DESCRIPTION cran
  • shiny >= 1.6.0 depends
  • shinyBS * depends
  • parallel * enhances
  • DT * imports
  • RColorBrewer * imports
  • config >= 0.3.1 imports
  • data.table * imports
  • dplyr * imports
  • golem >= 0.3.1 imports
  • grDevices * imports
  • graphics * imports
  • gridExtra * imports
  • methods * imports
  • plot3D * imports
  • plotly * imports
  • plyr * imports
  • pryr * imports
  • shinyFiles * imports
  • shinyjs * imports
  • stats * imports
  • stringdist * imports
  • stringr * imports
  • utils * imports
  • BiocGenerics * suggests
  • BiocManager * suggests
  • BiocStyle * suggests
  • Biostrings * suggests
  • RefManageR * suggests
  • biocthis * suggests
  • fs * suggests
  • knitr * suggests
  • motifStack * suggests
  • rlist * suggests
  • rmarkdown * suggests
  • shinycssloaders * suggests
  • testthat >= 3.0.0 suggests
  • tidyverse * suggests
  • xtable * suggests