Biocview "GraphAndNetwork"

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

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

AmiGO visualize R interface

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'.

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 visualizing complex biological network

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

A Systems Biology Approach for Drug Repurposing

a tool set for pathway based data integration and visualization

Batch Effects Quality Control Software

Bayesian Inference of Regulation of Transcriptional Activity

Benchmarking of several gene network inference methods

Better prediction by use of co-data: Adaptive group-regularized ridge regression

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

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

Co-expression Modules identification Tool

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

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

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

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

Display and manipulate graphs in Cytoscape

Display and manipulate graphs in Cytoscape >= 3.3.0

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

Efficient graph representation and manipulation in Bioconductor

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

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

Extending guilt by association by degree

FCBF-based Co-Expression Networks for Single Cells

Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

Find microbial interactions

Functional Network Analysis

Functions for Cytoscape Automation

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

GEne Network Inference with Ensemble of trees

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

Gene Regulatory Network Inference Using Time Series

Gene Set Enrichment Analysis with Networks

Gene set enrichment data structures and methods

gin in R

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 examples and use cases in Bioinformatics

GRAPH Interaction from pathway Topological Environment

graph support for KO, KEGG Orthology

Graph Theoretic Association Tests

GWAS Incorporating Networks

Hidden Variable Dynamic Modeling

Hierarchical ensemble method based on factor graph

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

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

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

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

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

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 Correlation Estimator and Statistical Inference Procedures.

Mutual Information NETworks

Neighbor_net analysis

netboxr

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 Perturbation Amplitude

Network-Regularized Regression Models

Network smoothing for scRNAseq

OmniPath web service client

OmniPath web service client and more

Overlay omics data onto SBGN pathway diagram

Package Dependency Tools

PaIRKAT

PANDA Algorithm

PathoStat Statistical Microbiome Analysis Package

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

Phenotypes and cellular organizational units

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

Protein co-expression network analysis (ProCoNA).

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

Protein-Protein Interaction Statistical Package

Proteomics Standard Initiative Common QUery InterfaCe

Provides plotting capabilities for R graph objects

Random walk with restart on multiplex and heterogeneous 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)

Render molecular pathways

Reproducible GSEA Benchmarking

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

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBML-R Interface and Analysis Tools

Seamless navigation through combined results of set-based and network-based enrichment 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

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

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Survival analysis using transcriptional networks inferred by the RTN package

Synthetic Lethal Genetic Interaction

Ternary Network Estimation

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 the FOBI Ontology

Topology-based pathway analysis of RNA-seq data

Transcriptional analysis based on transcriptograms

Transcriptional Rewiring

Transcription Factors Enrichment Analysis

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

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)

Biocview "GraphAndNetwork"

R Package Documentation

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