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

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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 <claudia.cava@ibfm.cnr.it>
License
GPL (>= 3)
Version
1.4.2
URLs

View on Bioconductor

Man pages

a
Ouput of the 1 network for 1 case study
a2
Ouput of the 1 network for 2 case study
b
Ouput of the 2 network for 1 case study
b2
Ouput of the 2 network for 2 case study
c
Ouput of the 3 network for 1 case study
c2
Ouput of the 3 network for 2 case study
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
d
Ouput of the 4 network for 1 case study
Data_CANCER_normUQ_filt
TCGA data for breast cancer
dataClin
clinical data for prostate cancer
dataFilt
TCGA data for prostate cancer afetr quantile analysis
net_shar_prot
Output of SpidermiRquery_spec_networks
org
Species supported by GeneMania
out_net
Output of SpidermiRdownload_net
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

Files in this package

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/a.rda
SpidermiR/data/a2.rda
SpidermiR/data/b.rda
SpidermiR/data/b2.rda
SpidermiR/data/c.rda
SpidermiR/data/c2.rda
SpidermiR/data/d.rda
SpidermiR/data/dataClin.rda
SpidermiR/data/dataFilt.rda
SpidermiR/data/datalist
SpidermiR/data/net_shar_prot.rda
SpidermiR/data/org.rda
SpidermiR/data/out_net.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/SpidermiR_pdf.R
SpidermiR/inst/doc/SpidermiR_pdf.Rmd
SpidermiR/inst/doc/SpidermiR_pdf.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/a.Rd
SpidermiR/man/a2.Rd
SpidermiR/man/b.Rd
SpidermiR/man/b2.Rd
SpidermiR/man/c.Rd
SpidermiR/man/c2.Rd
SpidermiR/man/d.Rd
SpidermiR/man/dataClin.Rd
SpidermiR/man/dataFilt.Rd
SpidermiR/man/net_shar_prot.Rd
SpidermiR/man/org.Rd
SpidermiR/man/out_net.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/SpidermiR_pdf.Rmd