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

Installation

source("https://bioconductor.org/biocLite.R")
biocLite("SpidermiR")

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Version

Version

1.1.8

License

GPL (>= 3)

Issues

2

Pull Requests

0

Stars

2

Forks

2

Maintainer

Claudia Cava

Last Published

February 15th, 2017

Functions in SpidermiR (1.1.8)

SpidermiRanalyze_mirna_extra_cir

Integration of Extracellular/Circulating miRNA
SpidermiRanalyze_Community_detection_bi

Community detection from biomarkers of interest
SpidermiRanalyze_mirnanet_pharm

Integration of pharmacomiR in the network
SpidermiRanalyze_direct_subnetwork

Searching by biomarkers of interest with direct interaction by ONLY the nodes in BI
SpidermiRanalyze_direct_net

Searching by biomarkers of interest with direct interaction
SpidermiRanalyze_Community_detection_net

Find the network of community detection and direct biormarker
SpidermiRanalyze_mirna_network

Integration of microRNA target networks.
SpidermiRanalyze_mirna_gene_complnet

Integration of microRNA target gene networks.
SpidermiRanalyze_Community_detection

Find community detection
SpidermiRanalyze_degree_centrality

Ranking degree centrality genes
SpidermiRquery_spec_networks

Searching by network categories
SpidermiRdownload_net

Download the network from GeneMania.
SpidermiRdownload_pharmacomir

Download both miRNA target and the gene-drug interaction from PharmacomiR database
SpidermiRdownload_miRNAprediction

Download miRNA predicted database
SpidermiRquery_networks_type

Network categories
SpidermiRdownload_miRNAvalidate

Download miRNA validated database
SpidermiRanalyze_subnetwork_neigh

Searching by biomarkers of interest and all the edges among this bunch of nodes
SpidermiRprepare_NET

Prepare matrix of gene network from Genamania with Ensembl Gene ID, and gene symbols
SpidermiRdownload_miRNAextra_cir

Download miRNA validated database
SpidermiRquery_disease

Visualize disease categories
SpidermiRvisualize_BI

Visualize results obtained by SpidermiR analysis starting form a set of biomarker of interest
SpidermiRvisualize_plot_target

Visualize results obtained by SpidermiRanalyze_mirna_network
SpidermiRvisualize_adj_matrix

plots the adjacency matrix of the network
SpidermiRquery_species

Searching by network species
SpidermiRvisualize_degree_dist

plots the degree distribution of the network
SpidermiRvisualize_mirnanet

Visualize results obtained by SpidermiR analysis
SpidermiRvisualize_3Dbarplot

plots the 3D barplot