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 bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-cellhts2:

>=2.66.0,<2.67.0

depends bioconductor-geneplotter:

>=1.80.0,<1.81.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-splots:

>=1.68.0,<1.69.0

depends r-abind:

depends r-base:

>=4.3,<4.4.0a0

depends r-gplots:

depends r-hwriter:

depends r-ics:

depends r-icsnp:

depends r-lattice:

depends r-latticeextra:

depends r-locfit:

depends r-rcolorbrewer:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-rnainteract

and update with::

   mamba update bioconductor-rnainteract

To create a new environment, run:

mamba create --name myenvname bioconductor-rnainteract

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-rnainteract/tags`_ for valid values for ``<tag>``)

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