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

## Documentation for package ‘SpidermiR’ version 1.7.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SpidermiR-package | Download data
Case_Study1_loading_1_network | Loading 1 network of shared protein domanin
Case_Study1_loading_2_network | Loading 2 network of shared protein domanin
Case_Study1_loading_3_network | Loading 3 network of shared protein domanin
Case_Study1_loading_4_network | Loading 4 network of shared protein domanin
Case_Study2_loading_1_network | Loading 1 network of Protein Interactions (PI)
Case_Study2_loading_2_network | Loading 2 network of Protein Interactions (PI) with miRNAs
Case_Study2_loading_3_network | Loading 3 network of Protein Interactions (PI) with miRNAs
SpidermiR | Download data
SpidermiRanalyze_Community_detection | Find community detection
SpidermiRanalyze_Community_detection_bi | Community detection from biomarkers of interest
SpidermiRanalyze_Community_detection_net | Find the network of community detection and direct biormarker
SpidermiRanalyze_degree_centrality | Ranking degree centrality genes
SpidermiRanalyze_DEnetworkTCGA | Integration with TCGA data in order to obtain a network of differentially expressed (DE) genes or miRNAs.
SpidermiRanalyze_direct_net | Searching by biomarkers of interest with direct interaction
SpidermiRanalyze_direct_subnetwork | Searching by biomarkers of interest with direct interaction by ONLY the nodes in BI
SpidermiRanalyze_mirnanet_pharm | Integration of pharmacomiR in the network
SpidermiRanalyze_mirna_gene_complnet | Integration of microRNA target gene networks.
SpidermiRanalyze_mirna_network | Integration of microRNA target networks.
SpidermiRanalyze_subnetwork_neigh | Searching by biomarkers of interest and all the edges among this bunch of nodes
SpidermiRdownload_miRNAextra_cir | Download miRNA validated database
SpidermiRdownload_miRNALNC_miRNA | Download microRNAs binding sites on long non coding RNA from lncRNome database
SpidermiRdownload_miRNALNC_RNA | Download Long Non-Coding RNA (LNC-RNA) from lncRNome database
SpidermiRdownload_miRNAprediction | Download miRNA predicted database
SpidermiRdownload_miRNAvalidate | Download miRNA validated database
SpidermiRdownload_net | Download the network from GeneMania.
SpidermiRdownload_pharmacomir | Download both miRNA target and the gene-drug interaction from PharmacomiR database
SpidermiRprepare_NET | Prepare matrix of gene network from Genamania with Ensembl Gene ID, and gene symbols
SpidermiRquery_disease | Visualize disease categories
SpidermiRquery_networks_type | Network categories
SpidermiRquery_species | Searching by network species
SpidermiRquery_spec_networks | Searching by network categories
SpidermiRvisualize_3Dbarplot | plots the 3D barplot
SpidermiRvisualize_adj_matrix | plots the adjacency matrix of the network
SpidermiRvisualize_BI | Visualize results obtained by SpidermiR analysis starting form a set of biomarker of interest
SpidermiRvisualize_degree_dist | plots the degree distribution of the network
SpidermiRvisualize_direction | Visualize results obtained by SpidermiR analysis with the direction of the interaction (pharmaco-gene and miRNA-gene)
SpidermiRvisualize_mirnanet | Visualize results obtained by SpidermiR analysis
SpidermiRvisualize_plot_target | Visualize results obtained by SpidermiRanalyze_mirna_network