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
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
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
Addon to CellNOptR: Fuzzy Logic
Addon to CellNOptR: Fuzzy Logic
Affinity Network Fusion for Complex Patient Clustering
Affinity Network Fusion for Complex Patient Clustering
A model for network-based prioritisation of genes
A model for network-based prioritisation of genes
An alternative to dendrogram visualization and insertion of multiple layers of information
An alternative to dendrogram visualization and insertion of multiple layers of information
An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
An interface to the BOOST graph library
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
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 Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
A package for visualizing complex biological network
A shiny user interface for rTRM
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
A Systems Biology Approach for Drug Repurposing
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
Base package for enabling powerful shiny web displays of Bioconductor objects
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)
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
Bioc2019PanCancerStudy
Biological Network Analysis
Biological Network Analysis
Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
Causal network analysis methods
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
CNCDriver
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
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Co-expression Modules identification Tool
Co-expression Modules identification Tool
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
CompositeDriver
Constraint based modeling in R using metabolic reconstruction databases
Constraint based modeling in R using metabolic reconstruction databases
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Convert a Graph into a D3js Script
CoRegFlux
CoRegFlux
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
Create 3D transomics network view with Çytoscape and Cy3D
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
Differential co-expression/association network analysis
Diffusion scores on biological networks
Diffusion scores on biological networks
Diffusion scores on biological networks
Display and manipulate graphs in Cytoscape >= 3.3.0
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
Dry lab for exploring miRNA-mRNA relationships
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
Extending guilt by association by degree
Extending guilt by association by degree
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Functional Gene Networks derived from biological enrichment analyses
Functional Network Analysis
Functional Network Analysis
Functional similarities
Functional similarities
Functions for Cytoscape Automation
Functions to Access and Control Cytoscape
Functions to Access and Control Cytoscape
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
Gene regulator enrichment analysis
Gene Regulatory Network Inference Using Time Series
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment Analysis with Networks
GenoMetric Query Language for R/Bioconductor
GenoMetric Query Language for R/Bioconductor
gin in R
gin in R
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GraphAlignment
GRAPH Interaction from pathway Topological Environment
GRAPH Interaction from pathway Topological Environment
Graph Theoretic Association Tests
GWAS Incorporating Networks
GWAS Incorporating Networks
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
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
Import Omnipath network
Import Omnipath network
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring unobserved perturbations from gene expression data
Infers biological signatures from gene expression data
Integrating microRNA expression into signaling pathways for pathway analysis
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 visualization and manipulation of nested networks
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interpretation and enrichment for metabolomics data
Interpretation and enrichment for metabolomics data
KinSwingR: network-based kinase activity prediction
KinSwingR: network-based kinase activity prediction
Landscape Expression Visualization Interface
Landscape Expression Visualization Interface
Landscape Single Cell Entropy
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
Linear model and normality based normalization and transformation method (Linnorm)
LiquidAssociation
Metabolite Set Enrichment Analysis (MSEA)
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Metadata management for multiomic specification of transcriptional regulatory networks
Metadata management for multiomic specification of transcriptional regulatory networks
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
microRNA-mRNA Integration, Analysis and Network Generation Tool
Mixture Nested Effects Models
Mixture Nested Effects Models
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
Modeling networks for individual samples using LIONESS
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Mutual Information NETworks
NDEx R client library
NDEx R client library
netboxr
netboxr
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 Analysis Supported by Boosting
Network-based Gene Prioritization Analysis (NetGPA)
Network-based pathway over-representation analysis (NetORA)
Network-based patient classifier
Network-based patient classifier
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
Network Centrality Metrics for Elastic-Net Regularized Models
Network Centrality Metrics for Elastic-Net Regularized Models
Network Perturbation Amplitude
Network Perturbation Amplitude
Network-Regularized Regression Models
Network-Regularized Regression Models
Network Seriation And Modularization
Network smoothing for scRNAseq
Network smoothing for scRNAseq
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
Outlier Protein and Phosphosite Target Identifier
Outlier Protein and Phosphosite Target Identifier
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
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
Phenotype Consensus ANalysis (PCAN)
Phenotype-driven module identification
Phenotype-driven module identification
Phenotypes and cellular organizational units
Pipeline for augmented co-expression analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Prediction of pathway-related protein-protein interaction networks
Principal Coordinates and Hotelling's T-Square method
Protein-Protein Interaction Statistical Package
Protein-Protein Interaction Statistical Package
Quantify deregulation of pathways in cancer
Random walk with restart on multiplex and heterogeneous Networks
Random walk with restart on multiplex and heterogeneous Networks
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Regression-based network inference using Bayesian Model Averaging
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
regutools: an R package for data extraction from RegulonDB
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
Routines for the functional analysis of biological networks
R package implementing the Cytoscape Exchange (CX) format
R support for SBML, using libsbml
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
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
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Single Cell Inference of Regulatory Activity
Sparse multiple canonical correlation network analysis tool
Sparse Multiple Canonical Correlation Network Analysis Tool
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
S-system parameter estimation method
StarBioTrek
StarBioTrek
StarBioTrek
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
Synthetic Expression Data for Gene Regulatory Network Inference
Synthetic Lethal Genetic Interaction
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
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"
The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
training of logical models from indirect measurements of perturbation experiments
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptional Data Guided fMRI Network Classification
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Two-sample tests on a graph
variant-transcription factor-phenotype networks
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
Visualize all edges within a KEGG pathway and overlay LINCS data
Visualize all edges within a KEGG pathway and overlay LINCS data [option]