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

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).

AuthorClaudia Cava, Antonio Colaprico, Alex Graudenzi, Gloria Bertoli, Tiago C. Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni
Date of publicationNone
MaintainerClaudia Cava <claudia.cava@ibfm.cnr.it>
LicenseGPL (>= 3)
Version1.4.7
https://github.com/claudiacava/SpidermiR

View on Bioconductor

Man pages

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

Functions

Case_Study1_loading_1_network Man page
Case_Study1_loading_2_network Man page
Case_Study1_loading_3_network Man page
Case_Study1_loading_4_network Man page
Case_Study2_loading_1_network Man page
Case_Study2_loading_2_network Man page
Case_Study2_loading_3_network Man page
Data_CANCER_normUQ_filt Man page
dataClin Man page
SpidermiR Man page
SpidermiRanalyze_Community_detection Man page
SpidermiRanalyze_Community_detection_bi Man page
SpidermiRanalyze_Community_detection_net Man page
SpidermiRanalyze_degree_centrality Man page
SpidermiRanalyze_DEnetworkTCGA Man page
SpidermiRanalyze_direct_net Man page
SpidermiRanalyze_direct_subnetwork Man page
SpidermiRanalyze_mirna_extra_cir Man page
SpidermiRanalyze_mirna_gene_complnet Man page
SpidermiRanalyze_mirnanet_pharm Man page
SpidermiRanalyze_mirna_network Man page
SpidermiRanalyze_subnetwork_neigh Man page
SpidermiRdownload_miRNAextra_cir Man page
SpidermiRdownload_miRNAprediction Man page
SpidermiRdownload_miRNAvalidate Man page
SpidermiRdownload_net Man page
SpidermiRdownload_pharmacomir Man page
SpidermiR-package Man page
SpidermiRprepare_NET Man page
SpidermiRquery_disease Man page
SpidermiRquery_networks_type Man page
SpidermiRquery_species Man page
SpidermiRquery_spec_networks Man page
SpidermiRvisualize_3Dbarplot Man page
SpidermiRvisualize_adj_matrix Man page
SpidermiRvisualize_BI Man page
SpidermiRvisualize_degree_dist Man page
SpidermiRvisualize_direction Man page
SpidermiRvisualize_mirnanet Man page
SpidermiRvisualize_plot_target Man page

Files

SpidermiR/DESCRIPTION
SpidermiR/NAMESPACE
SpidermiR/NEWS
SpidermiR/R
SpidermiR/R/Case_study1.R SpidermiR/R/SpidermiR.R SpidermiR/R/SpidermiRInternal.R SpidermiR/R/SpidermiRanalyze.R SpidermiR/R/SpidermiRdownload.R SpidermiR/R/SpidermiRprepare.R SpidermiR/R/SpidermiRquery.R SpidermiR/R/SpidermiRvisualize.R
SpidermiR/R/case_study2.r
SpidermiR/README.md
SpidermiR/build
SpidermiR/build/vignette.rds
SpidermiR/data
SpidermiR/data/Data_CANCER_normUQ_filt.rda
SpidermiR/data/dataClin.rda
SpidermiR/inst
SpidermiR/inst/CITATION
SpidermiR/inst/doc
SpidermiR/inst/doc/SpidermiR.R
SpidermiR/inst/doc/SpidermiR.Rmd
SpidermiR/inst/doc/SpidermiR.html
SpidermiR/inst/doc/SpidermiRcasestudy.R
SpidermiR/inst/doc/SpidermiRcasestudy.Rmd
SpidermiR/inst/doc/SpidermiRcasestudy.pdf
SpidermiR/man
SpidermiR/man/Case_Study1_loading_1_network.Rd SpidermiR/man/Case_Study1_loading_2_network.Rd SpidermiR/man/Case_Study1_loading_3_network.Rd SpidermiR/man/Case_Study1_loading_4_network.Rd SpidermiR/man/Case_Study2_loading_1_network.Rd SpidermiR/man/Case_Study2_loading_2_network.Rd SpidermiR/man/Case_Study2_loading_3_network.Rd SpidermiR/man/Data_CANCER_normUQ_filt.Rd SpidermiR/man/SpidermiR.Rd SpidermiR/man/SpidermiRanalyze_Community_detection.Rd SpidermiR/man/SpidermiRanalyze_Community_detection_bi.Rd SpidermiR/man/SpidermiRanalyze_Community_detection_net.Rd SpidermiR/man/SpidermiRanalyze_DEnetworkTCGA.Rd SpidermiR/man/SpidermiRanalyze_degree_centrality.Rd SpidermiR/man/SpidermiRanalyze_direct_net.Rd SpidermiR/man/SpidermiRanalyze_direct_subnetwork.Rd SpidermiR/man/SpidermiRanalyze_mirna_extra_cir.Rd SpidermiR/man/SpidermiRanalyze_mirna_gene_complnet.Rd SpidermiR/man/SpidermiRanalyze_mirna_network.Rd SpidermiR/man/SpidermiRanalyze_mirnanet_pharm.Rd SpidermiR/man/SpidermiRanalyze_subnetwork_neigh.Rd SpidermiR/man/SpidermiRdownload_miRNAextra_cir.Rd SpidermiR/man/SpidermiRdownload_miRNAprediction.Rd SpidermiR/man/SpidermiRdownload_miRNAvalidate.Rd SpidermiR/man/SpidermiRdownload_net.Rd SpidermiR/man/SpidermiRdownload_pharmacomir.Rd SpidermiR/man/SpidermiRprepare_NET.Rd SpidermiR/man/SpidermiRquery_disease.Rd SpidermiR/man/SpidermiRquery_networks_type.Rd SpidermiR/man/SpidermiRquery_spec_networks.Rd SpidermiR/man/SpidermiRquery_species.Rd SpidermiR/man/SpidermiRvisualize_3Dbarplot.Rd SpidermiR/man/SpidermiRvisualize_BI.Rd SpidermiR/man/SpidermiRvisualize_adj_matrix.Rd SpidermiR/man/SpidermiRvisualize_degree_dist.Rd SpidermiR/man/SpidermiRvisualize_direction.Rd SpidermiR/man/SpidermiRvisualize_mirnanet.Rd SpidermiR/man/SpidermiRvisualize_plot_target.Rd SpidermiR/man/dataClin.Rd
SpidermiR/tests
SpidermiR/tests/testthat
SpidermiR/tests/testthat.R
SpidermiR/tests/testthat/test-download.r
SpidermiR/tests/testthat/test-query.r
SpidermiR/vignettes
SpidermiR/vignettes/SpidermiR.Rmd
SpidermiR/vignettes/SpidermiRcasestudy.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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