recipe bioconductor-sponge

Sparse Partial Correlations On Gene Expression

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/SPONGE.html

License:

GPL (>=3)

Recipe:

/bioconductor-sponge/meta.yaml

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

package bioconductor-sponge

versions:

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0, 

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.4.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biomart:

>=2.56.0,<2.57.0

depends bioconductor-complexheatmap:

>=2.16.0,<2.17.0

depends bioconductor-mirbaseconverter:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

depends r-cvms:

depends r-data.table:

depends r-dorng:

depends r-dplyr:

depends r-expm:

depends r-foreach:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggridges:

depends r-glmnet:

depends r-grbase:

depends r-igraph:

depends r-iterators:

depends r-logging:

depends r-mass:

depends r-metbrewer:

depends r-ppcor:

depends r-randomforest:

depends r-rlang:

depends r-stringr:

depends r-tidyr:

depends r-tidyverse:

depends r-tnet:

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-sponge

and update with::

   mamba update bioconductor-sponge

To create a new environment, run:

mamba create --name myenvname bioconductor-sponge

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-sponge:<tag>

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

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