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, miR2Disease,miRTar, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).
|Author||Claudia Cava, Antonio Colaprico, Alex Graudenzi, Gloria Bertoli, Tiago C. Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni|
|Date of publication||None|
|Maintainer||Claudia Cava <firstname.lastname@example.org>|
|License||GPL (>= 3)|
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
Data_CANCER_normUQ_filt: TCGA data for breast cancer
dataClin: clinical data for prostate cancer
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...
SpidermiRanalyze_direct_net: Searching by biomarkers of interest with direct interaction
SpidermiRanalyze_direct_subnetwork: Searching by biomarkers of interest with direct interaction...
SpidermiRanalyze_mirna_extra_cir: Integration of Extracellular/Circulating miRNA
SpidermiRanalyze_mirna_gene_complnet: Integration of microRNA target gene networks.
SpidermiRanalyze_mirnanet_pharm: Integration of pharmacomiR in the network
SpidermiRanalyze_mirna_network: Integration of microRNA target networks.
SpidermiRanalyze_subnetwork_neigh: Searching by biomarkers of interest and all the edges among...
SpidermiRdownload_miRNAextra_cir: Download miRNA validated 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...
SpidermiRprepare_NET: Prepare matrix of gene network from Genamania with Ensembl...
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...
SpidermiRvisualize_degree_dist: plots the degree distribution of the network
SpidermiRvisualize_direction: Visualize results obtained by SpidermiR analysis with the...
SpidermiRvisualize_mirnanet: Visualize results obtained by SpidermiR analysis
SpidermiRvisualize_plot_target: Visualize results obtained by SpidermiRanalyze_mirna_network