Package Recipe 'bioconductor-rnainteract'

recipe bioconductor-rnainteract

Estimate Pairwise Interactions from multidimensional features

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/RNAinteract.html
License:: Artistic-2.0
Recipe:: /bioconductor-rnainteract/meta.yaml

RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.

package bioconductor-rnainteract¶

Versions:

1.50.0-0, 1.48.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.30.0-0,

1.50.0-0, 1.48.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.30.0-0, 1.28.0-0, 1.26.0-0

Depends:

on bioconductor-biobase >=2.62.0,<2.63.0
on bioconductor-cellhts2 >=2.66.0,<2.67.0
on bioconductor-geneplotter >=1.80.0,<1.81.0
on bioconductor-limma >=3.58.0,<3.59.0
on bioconductor-splots >=1.68.0,<1.69.0
on r-abind
on r-base >=4.3,<4.4.0a0
on r-gplots
on r-hwriter
on r-ics
on r-icsnp
on r-lattice
on r-latticeextra
on r-locfit
on r-rcolorbrewer

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-rnainteract

to add into an existing workspace instead, run:

pixi add bioconductor-rnainteract

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-rnainteract

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rnainteract

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-rnainteract:<tag>

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