SpidermiR: SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
Version 1.6.1

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).

Browse man pages Browse package API and functions Browse package files

AuthorClaudia Cava, Antonio Colaprico, Alex Graudenzi, Gloria Bertoli, Tiago C. Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni
Bioconductor views GeneRegulation Network miRNA
Date of publicationNone
MaintainerClaudia Cava <claudia.cava@ibfm.cnr.it>
LicenseGPL (>= 3)
Version1.6.1
URL https://github.com/claudiacava/SpidermiR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SpidermiR")

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Case_study1.R
R/SpidermiR.R
R/SpidermiRInternal.R
R/SpidermiRanalyze.R
R/SpidermiRdownload.R
R/SpidermiRprepare.R
R/SpidermiRquery.R
R/SpidermiRvisualize.R
R/case_study2.r
README.md
build
build/vignette.rds
data
data/Data_CANCER_normUQ_filt.rda
data/dataClin.rda
inst
inst/CITATION
inst/doc
inst/doc/SpidermiR.R
inst/doc/SpidermiR.Rmd
inst/doc/SpidermiR.html
inst/doc/SpidermiRcasestudy.R
inst/doc/SpidermiRcasestudy.Rmd
inst/doc/SpidermiRcasestudy.pdf
man
man/Case_Study1_loading_1_network.Rd
man/Case_Study1_loading_2_network.Rd
man/Case_Study1_loading_3_network.Rd
man/Case_Study1_loading_4_network.Rd
man/Case_Study2_loading_1_network.Rd
man/Case_Study2_loading_2_network.Rd
man/Case_Study2_loading_3_network.Rd
man/Data_CANCER_normUQ_filt.Rd
man/SpidermiR.Rd
man/SpidermiRanalyze_Community_detection.Rd
man/SpidermiRanalyze_Community_detection_bi.Rd
man/SpidermiRanalyze_Community_detection_net.Rd
man/SpidermiRanalyze_DEnetworkTCGA.Rd
man/SpidermiRanalyze_degree_centrality.Rd
man/SpidermiRanalyze_direct_net.Rd
man/SpidermiRanalyze_direct_subnetwork.Rd
man/SpidermiRanalyze_mirna_gene_complnet.Rd
man/SpidermiRanalyze_mirna_network.Rd
man/SpidermiRanalyze_mirnanet_pharm.Rd
man/SpidermiRanalyze_subnetwork_neigh.Rd
man/SpidermiRdownload_miRNAextra_cir.Rd
man/SpidermiRdownload_miRNAprediction.Rd
man/SpidermiRdownload_miRNAvalidate.Rd
man/SpidermiRdownload_net.Rd
man/SpidermiRdownload_pharmacomir.Rd
man/SpidermiRprepare_NET.Rd
man/SpidermiRquery_disease.Rd
man/SpidermiRquery_networks_type.Rd
man/SpidermiRquery_spec_networks.Rd
man/SpidermiRquery_species.Rd
man/SpidermiRvisualize_3Dbarplot.Rd
man/SpidermiRvisualize_BI.Rd
man/SpidermiRvisualize_adj_matrix.Rd
man/SpidermiRvisualize_degree_dist.Rd
man/SpidermiRvisualize_direction.Rd
man/SpidermiRvisualize_mirnanet.Rd
man/SpidermiRvisualize_plot_target.Rd
man/dataClin.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-download.r
tests/testthat/test-query.r
vignettes
vignettes/SpidermiR.Rmd
vignettes/SpidermiRcasestudy.Rmd
SpidermiR documentation built on May 20, 2017, 9:51 p.m.