Biocview "Network"

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Add-on of the SQUAD Software
Add-on of the SQUAD Software
Addon to CellNOptR: Fuzzy Logic
Addon to CellNOptR: Fuzzy Logic
A model for network-based prioritisation of genes
A model for network-based prioritisation of genes
A model for network-based prioritisation of genes
An interface to the BOOST graph library
An interface to the BOOST graph library
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
An R package for pathway analysis using topological information
An R package for pathway analysis using topological information
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for qualitative biclustering in support of gene co-expression analyses
An R package to perform the network enrichment analysis (NEA).
A package for visualizing complex biological network
A package for visualizing complex biological network
A shiny user interface for rTRM
A shiny user interface for rTRM
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian Inference of Regulatory Influence on Expression (biRte)
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Causal network analysis methods
Causal network analysis methods
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
Constraint based modeling in R using metabolic reconstruction databases
Constraint based modeling in R using metabolic reconstruction databases
Convert a Graph into a D3js Script
Convert a Graph into a D3js Script
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
DeMAND
DeMAND
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Diffusion scores on biological networks
Display and manipulate graphs in Cytoscape >= 3.3.0
Display and manipulate graphs in Cytoscape >= 3.3.0
Display and manipulate graphs in Cytoscape >= 3.3.0
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
Dry lab for exploring miRNA-mRNA relationships
Dry lab for exploring miRNA-mRNA relationships
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
epiNEM
Extending guilt by association by degree
Extending guilt by association by degree
Functional Gene Networks derived from biological enrichment analyses
Functional Gene Networks derived from biological enrichment analyses
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functional similarities
Functional similarities
Functional similarities
GEne Network Inference with Ensemble of trees
Gene Regulatory Network Inference Using Time Series
Gene Regulatory Network Inference Using Time Series
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GraphAlignment
GraphAlignment
GRAPH Interaction from pathway Topological Environment
GRAPH Interaction from pathway Topological Environment
Graph Theoretic Association Tests
Graph Theoretic Association Tests
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)
Identification of transcriptional regulatory modules from PPI networks
Identification of transcriptional regulatory modules from PPI networks
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Infers biological signatures from gene expression data
Infers biological signatures from gene expression data
Integrating microRNA expression into signaling pathways for pathway analysis
Integrating microRNA expression into signaling pathways for pathway analysis
Integration of Disease Similarity Methods
Integration of Disease Similarity Methods
Integration of Disease Similarity Methods
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive visualization and manipulation of nested networks
Interactive visualization and manipulation of nested networks
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
LiquidAssociation
LiquidAssociation
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Methylation regulation network inference with Conditional Mutual information based PC-algorithem
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Mutual Information NETworks
Mutual Information NETworks
NDEx R client library
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
Network-Regularized Regression Models
Network Seriation And Modularization
Network Seriation And Modularization
OnASSIs Ontology Annotation and Semantic SImilarity software
Package for enabling powerful shiny web displays of Bioconductor objects
Package for enabling powerful shiny web displays of Bioconductor objects
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Phenotype Consensus ANalysis (PCAN)
Phenotype Consensus ANalysis (PCAN)
Phenotypes and cellular organizational units
Phenotypes and cellular organizational units
Prediction of pathway-related protein-protein interaction networks
Prediction of pathway-related protein-protein interaction networks
Principal Coordinates and Hotelling's T-Square method
Principal Coordinates and Hotelling's T-Square method
Protein-Protein Interaction Statistical Package
Protein-Protein Interaction Statistical Package
Quantify deregulation of pathways in cancer
Quantify deregulation of pathways in cancer
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
Regression-based network inference using Bayesian Model Averaging
Regression-based network inference using Bayesian Model Averaging
Routines for the functional analysis of biological networks
Routines for the functional analysis of biological networks
R support for SBML, using libsbml
R support for SBML, using libsbml
SBML-R Interface and Analysis Tools
SBML-R Interface and Analysis Tools
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Spatial Analysis of Network Associations
Spatial Analysis of Network Associations
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
S-system parameter estimation method
S-system parameter estimation method
StarBioTrek
StarBioTrek
StarBioTrek
StarTrek
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
Synthetic Expression Data for Gene Regulatory Network Inference
Synthetic Lethal Genetic Interaction
Synthetic Lethal Genetic Interaction
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
training of logical models from indirect measurements of perturbation experiments
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Two-sample tests on a graph
Two-sample tests on a graph
variant-transcription factor-phenotype networks
variant-transcription factor-phenotype networks
Visualization of multi-dimentional cancer genomics data
Visualization of multi-dimentional cancer genomics data
Visualization of multi-dimentional cancer genomics data
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]