recipe bioconductor-mirsponger

Identification and analysis of miRNA sponge regulation

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-mirsponger/meta.yaml

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

package bioconductor-mirsponger

versions:

2.4.0-0,  2.2.0-1,  2.2.0-0,  1.20.1-1,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.2-0,  1.16.0-0, 

2.4.0-0,  2.2.0-1,  2.2.0-0,  1.20.1-1,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.2-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.1-0

depends bioconductor-clusterprofiler:

>=4.8.0,<4.9.0

depends bioconductor-dose:

>=3.26.0,<3.27.0

depends bioconductor-org.hs.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-reactomepa:

>=1.44.0,<1.45.0

depends bioconductor-sponge:

>=1.22.0,<1.23.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-corpcor:

depends r-doparallel:

depends r-foreach:

depends r-igraph:

depends r-linkcomm:

depends r-mcl:

depends r-rcpp:

depends r-survival:

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-mirsponger

and update with::

   mamba update bioconductor-mirsponger

To create a new environment, run:

mamba create --name myenvname bioconductor-mirsponger

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-mirsponger:<tag>

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

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