Package Recipe 'bioconductor-spidermir'

recipe bioconductor-spidermir

SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/SpidermiR.html
License:: GPL (>= 3)
Recipe:: /bioconductor-spidermir/meta.yaml
Links:: biotools: spidermir, doi: 10.3390/ijms18020274

The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miRTarBase, miRandola, Miranda, PicTar and TargetScan). Furthermore, we also present a statistical test to identify pharmaco-mir relationships using the gene-drug interactions derived by DGIdb and MATADOR database.

package bioconductor-spidermir¶

Versions:

1.32.0-0, 1.30.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-0,

1.32.0-0, 1.30.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-1, 1.12.0-0, 1.10.0-0, 1.8.2-0

Depends:

on bioconductor-annotationdbi >=1.64.0,<1.65.0
on bioconductor-mirnatap >=1.36.0,<1.37.0
on bioconductor-mirnatap.db >=0.99.0,<0.100.0
on bioconductor-org.hs.eg.db >=3.18.0,<3.19.0
on r-base >=4.3,<4.4.0a0
on r-gdata
on r-httr
on r-igraph

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-spidermir

to add into an existing workspace instead, run:

pixi add bioconductor-spidermir

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-spidermir

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-spidermir

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-spidermir:<tag>

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