Package Recipe 'bioconductor-scanmirapp'

recipe bioconductor-scanmirapp

scanMiR shiny application

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/scanMiRApp.html
License:: GPL-3
Recipe:: /bioconductor-scanmirapp/meta.yaml

A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

package bioconductor-scanmirapp¶

Versions:

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

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationfilter >=1.34.0,<1.35.0
on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-ensembldb >=2.34.0,<2.35.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scanmir >=1.16.0,<1.17.0
on bioconductor-scanmirdata >=1.16.0,<1.17.0
on bioconductor-txdbmaker >=1.6.0,<1.7.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-digest
on r-dt
on r-fst
on r-ggplot2
on r-htmlwidgets
on r-matrix
on r-plotly
on r-rintrojs
on r-shiny
on r-shinycssloaders
on r-shinydashboard
on r-shinyjqui
on r-waiter

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-scanmirapp

to add into an existing workspace instead, run:

pixi add bioconductor-scanmirapp

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-scanmirapp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scanmirapp

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-scanmirapp:<tag>

(see bioconductor-scanmirapp/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-scanmirapp/README.html)