Biocview "Network"

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

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Adaptive Dropout Imputer (ADImpute)

Add-on of the SQUAD Software

Addon to CellNOptR: Fuzzy Logic

Affinity Network Fusion for Complex Patient Clustering

A model for network-based prioritisation of genes

An alternative to dendrogram visualization and insertion of multiple layers of information

Analysis and Visualisation of the Human Phenotype Ontology

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

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

A Systems Biology Approach for Drug Repurposing

A Toolkit for Flow And Mass Cytometry Data

A tool set for 3D Trans-Omic network visualization with Cytoscape

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

Benchmarking of several gene network inference methods

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Bioc2019PanCancerStudy

Biological Network Analysis

Biological Network Reconstruction Omnibus

Candidate Gene Miner

Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information

Causal network analysis methods

Cell Signalling Using Single Cell RNAseq Data Analysis

Classification of RNA Sequences using Complex Network and Information Theory

CNCDriver

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

Co-expression Modules identification Tool

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

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Constraint based modeling in R using metabolic reconstruction databases

Constructing gene regulatory networks from expression data through functional module inference

Contains utils for loading and manipulating two-layers structure network models

Convert a Graph into a D3js Script

CoRegFlux

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

COSMOS (Causal Oriented Search of Multi-Omic Space)

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

Create Networks of Dendrochronological Series using Pairwise Similarity

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DeMAND

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

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 >= 3.3.0

Displaying binary trees with focus on dendrogram leaves

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

Dry lab for exploring miRNA-mRNA relationships

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

epiNEM

Extending guilt by association by degree

FCBF-based Co-Expression Networks for Single Cells

fedupShiny

Finding an Active Metabolic Module in Atom Transition Network

Fisher's Test for Enrichment and Depletion of User-Defined Pathways

From functional enrichment results to biological networks

Functional Gene Networks derived from biological enrichment analyses

Functional Network Analysis

Functional similarities

Functions for Cytoscape Automation

Functions to Access and Control Cytoscape

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

GEne Network Inference with Ensemble of trees

Gene regulator enrichment analysis

Gene Regulatory Network Inference Using Time Series

Gene Set Enrichment Analysis with Networks

Genetic inteRaction and EssenTiality neTwork mApper

GenoMetric Query Language for R/Bioconductor

gin in R

GO-terms Semantic Similarity Measures

GraphAlignment

GRAPH Interaction from pathway Topological Environment

Graph Theoretic Association Tests

GWAS Incorporating Networks

Hierarchical ensemble method based on factor graph

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)

Host-Pathogen Interaction Prediction

Identification of transcriptional regulatory modules from PPI networks

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

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

Inference And Analysis Of Synteny Networks

Inference of gene regulatory networks from gene expression data

Inferring functionally related proteins using protein interaction networks

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

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

Integration of Disease Similarity Methods

Integrative analysis of multi-omics data to infer regulatory networks

Integrative analysis of the microbiome and metabolome

Interactive Multi-Omics Cancers Data Visualization and Analysis

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

IReNA

KinSwingR: network-based kinase activity prediction

Landscape Expression Visualization Interface

Landscape Single Cell Entropy

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Linear model and normality based normalization and transformation method (Linnorm)

Lipid reaction prediction based on WormJam

LiquidAssociation

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

Metadata management for multiomic specification of transcriptional regulatory networks

Metadata management for multiomic specification of transcriptional regulatory networks, version 2

MethylMix: Identifying methylation driven cancer genes

Microbiome Data Simulation

Mixture Nested Effects Models

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)

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Molecular Signature identification using Biclustering

Multi Omic Master Regulator Analysis

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multi-Omics (time-course) network-based integration and interpretation

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Mutual Information NETworks

NDEx R client library

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-based patient classifier

Network-based prioritization of putative metabolite IDs

Network Centrality Metrics for Elastic-Net Regularized Models

Network Perturbation Amplitude

Network-Regularized Regression Models

Network Seriation And Modularization

Network smoothing for scRNAseq

OmniPath web service client

OmniPath web service client and more

OnASSIs Ontology Annotation and Semantic SImilarity software

Outlier Protein and Phosphosite Target Identifier

Package for CTDbase data query, visualization and downstream analysis

Package for enabling powerful shiny web displays of Bioconductor objects

PaIRKAT

PANDA Algorithm

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Perform co-DE gene analysis

PhenoGeneRanker: A gene and phenotype prioritization tool

Phenotype Consensus ANalysis (PCAN)

Phenotype-driven module identification

Phenotypes and cellular organizational units

Pipeline for augmented co-expression analysis

plot bayesian network inferred from gene expression data based on enrichment analysis results

PoTRA: Pathways of Topological Rank Analysis

Prediction of pathway-related protein-protein interaction networks

Principal Coordinates and Hotelling's T-Square method

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

Protein-Protein Interaction Statistical Package

Quantify deregulation of pathways in cancer

Random walk with restart on multiplex and heterogeneous Networks

Rapid Integration of Term Annotation and Network resources

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

Reduce + Visualize GO

Regression-based network inference using Bayesian Model Averaging

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

regutools: an R package for data extraction from RegulonDB

Reproducible GSEA Benchmarking

R implementation of Information measures

R implementation of informtion measures

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

SBML-R Interface and Analysis Tools

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

Signature-based Clustering for Diagnostic Purposes

Significance-based Modules Integrating the Transcriptome and Epigenome

Single Cell Entropy

Single Cell Inference of Regulatory Activity

Sparse Multiple Canonical Correlation Network Analysis Tool

Spatial Analysis of Network Associations

spatialHeatmap

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data

S-system parameter estimation method

StarBioTrek

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

Systematic quality checks on comparative genomics analyses

Systems EPigenomics Inference of Regulatory Activity

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

Ternary Network Estimation

The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways

Time sensitive microRNA-mRNA integration, analysis and network generation tool

tool to run PHONEMeS on phosphoproteomic 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 Data Guided fMRI Network Classification

TRONCO, an R package for TRanslational ONCOlogy

Two-sample tests on a graph

Unified methods for the inference and analysis of gene regulatory networks

Untargeted LC-MS data annotation

variant-transcription factor-phenotype networks

Visualising Set Enrichment Analysis Results

visualization and interpretation of textual information from omics summary data through network analysis

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 [option]

Weighting protein-protein interactions

Workflow for constructing Pathway-Gene-Transcript expression networks

Biocview "Network"

R Package Documentation

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