recipe bioconductor-panomir

Detection of miRNAs that regulate interacting groups of pathways

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/PanomiR.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-panomir/meta.yaml

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

package bioconductor-panomir

versions:

1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-clusterprofiler:

>=4.14.0,<4.15.0

depends bioconductor-gseabase:

>=1.68.0,<1.69.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-org.hs.eg.db:

>=3.20.0,<3.21.0

depends bioconductor-preprocesscore:

>=1.68.0,<1.69.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-forcats:

depends r-igraph:

depends r-metap:

depends r-rcolorbrewer:

depends r-rlang:

depends r-tibble:

depends r-withr:

requirements:

additional platforms:

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-panomir

and update with::

   mamba update bioconductor-panomir

To create a new environment, run:

mamba create --name myenvname bioconductor-panomir

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-panomir:<tag>

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

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