Package Recipe 'bioconductor-mirsponger'

recipe bioconductor-mirsponger

Identification and analysis of miRNA sponge regulation

Homepage:: https://bioconductor.org/packages/3.20/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:

2.14.1-0, 2.10.0-0, 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,

2.14.1-0, 2.10.0-0, 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:

on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-clusterprofiler >=4.18.4,<4.19.0a0
on bioconductor-dose >=4.4.0,<4.5.0
on bioconductor-dose >=4.4.0,<4.5.0a0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0a0
on bioconductor-reactomepa >=1.54.0,<1.55.0
on bioconductor-reactomepa >=1.54.0,<1.55.0a0
on bioconductor-sponge >=1.32.0,<1.33.0
on bioconductor-sponge >=1.32.0,<1.33.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-corpcor
on r-doparallel
on r-foreach
on r-igraph
on r-mcl
on r-rcolorbrewer
on r-rcpp
on r-survival

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-mirsponger

to add into an existing workspace instead, run:

pixi add bioconductor-mirsponger

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-mirsponger

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mirsponger

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-mirsponger:<tag>

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