Biocview "GraphAndNetwork"

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
A bioconductor package for high-dimensional exploration of biological network heterogeneity
A bioconductor package for high-dimensional exploration of biological network heterogeneity
Add-on of the SQUAD Software
Add-on of the SQUAD Software
Affected pathway ranking in differential gene expression analysis
AmiGO visualize R interface
AmiGO visualize R interface
analysis of co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
Analysis of co-regulatory network motifs and inference of 'dual regulons'
An interface to the BOOST graph library
An interface to the BOOST graph library
An R Package for retrieving data from DAVID into R objects using Web Services API.
An R Package for retrieving data from DAVID into R objects using Web Services API.
A package for visualizing complex biological network
A package for visualizing complex biological network
A package providing hypergraph data structures
A package providing hypergraph data structures
A queryable collection of molecular interactions, from many sources
A queryable collection of molecular interactions, from many sources
A shiny user interface for rTRM
A shiny user interface for rTRM
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
Batch Effects Quality Control Software
Batch Effects Quality Control Software
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulation of Transcriptional Activity
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Broadcast data between R and Gaggle
Broadcast data between R and Gaggle
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Causal network analysis methods
Causal network analysis methods
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
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
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
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
Denoising Algorithm based on Relevance network Topology
Denoising Algorithm based on Relevance network Topology
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
Diffusion scores on biological networks
Diffusion scores on biological networks
Display and manipulate graphs in Cytoscape
Display and manipulate graphs in Cytoscape
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
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in cytoscape.js
Distinguish direct and indirect interactions with Graphical Modelling
Distinguish direct and indirect interactions with Graphical Modelling
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Estimate protein complex membership using AP-MS protein data
Estimate protein complex membership using AP-MS protein data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Extending guilt by association by degree
Extending guilt by association by degree
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Finds Gene Co-expression Modules
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to handle cDNA microarray data, including several methods of data analysis
GEne Network Inference with Ensemble of trees
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Gene Regulatory Network Inference Using Time Series
Gene Regulatory Network Inference Using Time Series
Gene set enrichment data structures and methods
Gene set enrichment data structures and methods
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GraphAlignment
GraphAlignment
graph: A package to handle graph data structures
graph: A package to handle graph data structures
Graph examples and use cases in Bioinformatics
Graph examples and use cases in Bioinformatics
GRAPH Interaction from pathway Topological Environment
GRAPH Interaction from pathway Topological Environment
graph support for KO, KEGG Orthology
graph support for KO, KEGG Orthology
Graph Theoretic Association Tests
Graph Theoretic Association Tests
Hidden Variable Dynamic Modeling
Hidden Variable Dynamic Modeling
Identification of transcriptional regulatory modules from PPI networks
Identification of transcriptional regulatory modules from PPI networks
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference for predictive networks designed for (but not limited to) genomic data
Inference for predictive networks designed for (but not limited to) genomic data
Infers biological signatures from gene expression data
Infers biological signatures from gene expression data
In Silico Interactome
In Silico Interactome
Integrating microRNA expression into signaling pathways for pathway analysis
Integrating microRNA expression into signaling pathways for pathway analysis
Interaction Based Homogeneity for Evaluating Gene Lists
Interaction Based Homogeneity for Evaluating Gene Lists
Interactive visualization and manipulation of nested networks
Interactive visualization and manipulation of nested networks
JODA algorithm for quantifying gene deregulation using knowledge
JODA algorithm for quantifying gene deregulation using knowledge
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
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
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
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
Microbial Comparative Genomics in R
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Model-View-Controller (MVC) Classes
Model-View-Controller (MVC) Classes
Model-View-Controller (MVC) Classes That Use Biobase
Model-View-Controller (MVC) Classes That Use Biobase
Multiple comparison test visualization
Multiple comparison test visualization
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Multivariate Correlation Estimator and Statistical Inference Procedures.
Multivariate Correlation Estimator and Statistical Inference Procedures.
Mutual Information NETworks
Mutual Information NETworks
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
Package Dependency Tools
Package Dependency Tools
Package for Topology-based Pathway Analysis of RNASeq data
Package for Topology-based Pathway Analysis of RNASeq data
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Pathways from the NCI Pathways Database
Pathways from the NCI Pathways Database
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
Phenotypes and cellular organizational units
Phenotypes and cellular organizational units
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Protein co-expression network analysis (ProCoNA).
Protein co-expression network analysis (ProCoNA).
Protein-Protein Interaction Statistical Package
Protein-Protein Interaction Statistical Package
Proteomics Standard Initiative Common QUery InterfaCe
Proteomics Standard Initiative Common QUery InterfaCe
Provides plotting capabilities for R graph objects
Provides plotting capabilities for R graph objects
Provides plotting capabilities for R graph objects
R-Causal Library
Reconstruction of transcriptional networks and analysis of master regulators
Reconstruction of transcriptional networks and analysis of master regulators
Render molecular pathways
Render molecular pathways
Routines for the functional analysis of biological networks
Routines for the functional analysis of biological networks
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
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
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
signet: Selection Inference in Gene NETworks
SPADE -- An analysis and visualization tool for Flow Cytometry
Survival analysis using transcriptional networks inferred by the RTN package
Survival analysis using transcriptional networks inferred by the RTN package
Synthetic Lethal Genetic Interaction
Synthetic Lethal Genetic Interaction
Ternary Network Estimation
Ternary Network Estimation
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Tools for manipulating GO and microarrays.
Tools for manipulating GO and microarrays.
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
User-friendly version of GIN (GWAS Incorporating Networks).
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]
Visualizing Hypergaphs
Visualizing Hypergaphs