recipe bioconductor-spidermir

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

Homepage

https://bioconductor.org/packages/3.12/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

1.20.0-0,  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

• bioconductor-annotationdbi >=1.52.0,<1.53.0

• bioconductor-mageckflute >=1.10.0,<1.11.0

• bioconductor-mirnatap >=1.23.0,<1.24.0

• bioconductor-mirnatap.db >=0.99.0,<0.100.0

• bioconductor-org.hs.eg.db >=3.12.0,<3.13.0

• bioconductor-tcgabiolinks >=2.18.0,<2.19.0

• r-base >=4.0,<4.1.0a0

• r-gdata

• r-ggplot2

• r-gplots

• r-gridextra

• r-httr

• r-igraph

• r-lattice

• r-latticeextra

• r-networkd3

• r-visnetwork

Required By

• bioconductor-starbiotrek

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-spidermir

and update with:

conda update bioconductor-spidermir

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-spidermir:<tag>

(see bioconductor-spidermir/tags for valid values for <tag>)

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)