recipe bioconductor-spidermir

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,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).

Homepage

https://bioconductor.org/packages/3.9/bioc/html/SpidermiR.html

License

GPL (>= 3)

Recipe

/bioconductor-spidermir/meta.yaml

Links

biotools: spidermir, doi: 10.3390/ijms18020274

package bioconductor-spidermir

(downloads) docker_bioconductor-spidermir

Versions

1.12.0-0, 1.10.0-0, 1.8.2-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-mirnatap

>=1.16.0,<1.17.0

Depends bioconductor-mirnatap.db

>=0.99.0,<0.100.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-tcgabiolinks

>=2.10.0,<2.11.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-gdata

Depends r-ggplot2

Depends r-gplots

Depends r-gridextra

Depends r-httr

Depends r-igraph

Depends r-lattice

Depends r-latticeextra

Depends r-networkd3

Depends r-visnetwork

Requirements

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>)