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
A bioconductor package for high-dimensional exploration of biological network heterogeneity
A bioconductor package for high-dimensional exploration of biological network heterogeneity
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Add-on of the SQUAD Software
A fast hierarchical graph-based clustering method
Affected pathway ranking in differential gene expression analysis
Affinity Network Fusion for Complex Patient Clustering
Affinity Network Fusion for Complex Patient Clustering
AmiGO visualize R interface
An alternative to dendrogram visualization and insertion of multiple layers of information
An alternative to dendrogram visualization and insertion of multiple layers of information
Analysis and Visualisation of the Human Phenotype Ontology
Analysis of co-regulation 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 R Package for retrieving data from DAVID into R objects using Web Services API.
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
A package for visualization and extract details
A package for visualization and extract details
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 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 tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
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
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
Biological Network Analysis
Biological Network Analysis
Biological Network Reconstruction Omnibus
Broadcast data between R and Gaggle
Build Haplotye and Generate Figures
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
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
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
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
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)
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
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
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
Create Networks of Dendrochronological Series using Pairwise Similarity
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
Differential cell-type-specific allelic imbalance
Differential co-expression/association network analysis
Differential gene co-expression
Differentially Expressed Gene-Gene pairs
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 >= 3.3.0
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in cytoscape.js
Displaying binary trees with focus on dendrogram leaves
Distinguish direct and indirect interactions with Graphical Modelling
Do 16s Data Analysis and Generate Figures
Do 16s Data Analysis and Generate Figures
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Enrichment Analysis using Multiple Ontologies and False Discovery Rate
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
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
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Find microbial interactions
Functional Network Analysis
Functional Network Analysis
Functions for Cytoscape Automation
Functions to Access and Control Cytoscape
Functions to Access and Control Cytoscape
Functions to handle cDNA microarray data, including several methods of data analysis
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
Generalized correlation analysis and model construction strategy for metabolome and microbiome
Generalized correlation analysis and model construction strategy for metabolome and microbiome
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 Set Enrichment Analysis with Networks
Gene Set Enrichment Analysis with Networks
Gene set enrichment data structures and methods
Gene set enrichment data structures and methods
gin in R
gin in R
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
GraphAlignment
graph: A package to handle graph data structures
graph: A package to handle graph data structures
graph: A package to handle graph data structures
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 Theoretic Association Tests
GWAS Incorporating Networks
GWAS Incorporating Networks
Hidden Variable Dynamic Modeling
Hierarchical ensemble method based on factor graph
HiPathia: High-throughput Pathway Analysis
HiPathia: High-throughput Pathway Analysis
HiPathia: High-throughput Pathway Analysis
Identification of transcriptional regulatory modules from PPI networks
Inference And Analysis Of Synteny Networks
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 of gene regulatory networks from gene expression data
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Infers biological signatures from gene expression data
In Silico Interactome
Integrating microRNA expression into signaling pathways for pathway analysis
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
Interaction Based Homogeneity for Evaluating Gene Lists
Interactive visualization and manipulation of nested networks
Interface for the Reactome Graph Database
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
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
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Metabolite Set Enrichment Analysis (MSEA)
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
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 That Use Biobase
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
Motif Analysis In Gene Regulatory Networks
Multi-Omics (time-course) network-based integration and interpretation
Multiple comparison test visualization
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Multivariate Correlation Estimator and Statistical Inference Procedures.
Mutual Information NETworks
Neighbor_net analysis
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 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 smoothing for scRNAseq
Network smoothing for scRNAseq
OmniPath web service client
OmniPath web service client and more
Overlay omics data onto SBGN pathway diagram
Package Dependency Tools
Package Dependency Tools
PaIRKAT
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Pathway Enrichment Based on Differential Causal Effects
Pathway Enrichment Based on Differential Causal Effects
Pathway enrichment using a regularized regression approach
Pathways from the NCI Pathways Database
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Perform co-DE gene analysis
PhenoGeneRanker: A gene and phenotype prioritization tool
Phenotype-driven module identification
Phenotype-driven module identification
Phenotypes and cellular organizational units
Pipeline for augmented co-expression analysis
Pipeline for augmented co-expression analysis
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Protein co-expression network analysis (ProCoNA).
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
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
Random walk with restart on multiplex and heterogeneous Networks
Random walk with restart on multiplex and heterogeneous Networks
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
R-Causal Library
Recovering spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data.
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Render molecular pathways
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
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 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
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
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
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
signet: Selection Inference in Gene NETworks
signet: Selection Inference in Gene NETworks
Single-cell Targetted Network Inference
spatialHeatmap
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
Spatial quantile normalization
Spatial quantile normalization
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
Survival analysis using transcriptional networks inferred by the RTN package
Survival analysis using transcriptional networks inferred by the RTN package
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
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Tools for Manipulating the FOBI Ontology
Tools for Manipulating the FOBI Ontology
Tools for Manipulating the FOBI Ontology
Topology-based pathway analysis of RNA-seq data
Topology-based pathway analysis of RNA-seq data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptional Rewiring
Transcription Factors Enrichment Analysis
Transcription Factors Enrichment Analysis
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Two-sample tests on a graph
Unified methods for the inference and analysis of gene regulatory networks
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
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]
Visualizing Hypergaphs
Weighting protein-protein interactions
What the Package Does (One Line, Title Case)