Package Recipe 'bioconductor-tripr'

recipe bioconductor-tripr

T-cell Receptor/Immunoglobulin Profiler (TRIP)

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/tripr.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-tripr/meta.yaml

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.

package bioconductor-tripr¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-1, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.0-0

Depends:

on r-base >=4.5,<4.6.0a0
on r-config >=0.3.1
on r-data.table
on r-dplyr
on r-dt
on r-golem >=0.3.1
on r-gridextra
on r-plot3d
on r-plotly
on r-plyr
on r-rcolorbrewer
on r-shiny >=1.6.0
on r-shinybs
on r-shinyfiles
on r-shinyjs
on r-stringdist
on r-stringr
on r-vegan

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-tripr

to add into an existing workspace instead, run:

pixi add bioconductor-tripr

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-tripr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-tripr

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-tripr:<tag>

(see bioconductor-tripr/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tripr/README.html)