R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

sirusb/R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

nethet

A bioconductor package for high-dimensional exploration of biological network heterogeneity

FrankD/nethet

A bioconductor package for high-dimensional exploration of biological network heterogeneity

cannin/paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

BioPAX/paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

SQUADD

Add-on of the SQUAD Software

XuegongLab/HGC

A fast hierarchical graph-based clustering method

bhatturam/prius

Affected pathway ranking in differential gene expression analysis

ANF

Affinity Network Fusion for Complex Patient Clustering

BeautyOfWeb/ANF

Affinity Network Fusion for Complex Patient Clustering

RamiGO

AmiGO visualize R interface

leonardokume/TreeAndLeaf

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

TreeAndLeaf

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

neurogenomics/HPOExplorer

Analysis and Visualisation of the Human Phenotype Ontology

RTNduals

Analysis of co-regulation and inference of 'dual regulons'

chagasVinicius/RTNduals

analysis of co-regulatory network motifs and inference of 'dual regulons'.

chagasVinicius/RTNduals-alpha

analysis of co-regulatory network motifs and inference of 'dual regulons'.

chagasVinicius/RTNmotifs

analysis of co-regulatory network motifs and inference of 'dual regulons'.

RBGL

An interface to the BOOST graph library

RDAVIDWebService

An R Package for retrieving data from DAVID into R objects using Web Services API.

PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis

SCCC-BBC/PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

VennDetail

A package for visualization and extract details

guokai8/VennDetail

A package for visualization and extract details

netbiov

A package for visualizing complex biological network

Bioconductor/hypergraph

A package providing hypergraph data structures

hypergraph

A package providing hypergraph data structures

RefNet

A queryable collection of molecular interactions, from many sources

rTRMui

A shiny user interface for rTRM

ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

nachoryu/ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

azampvd/DrugDiseaseNet

A Systems Biology Approach for Drug Repurposing

pathview

a tool set for pathway based data integration and visualization

BowenNCSU/pathview

a tool set for pathway based data integration and visualization

mmoisse/pathview

a tool set for pathway based data integration and visualization

datapplab/pathview

a tool set for pathway based data integration and visualization

DGendooLab/pathviewM

a tool set for pathway based data integration and visualization

BatchQC

Batch Effects Quality Control Software

compbiomed/BatchQC

Batch Effects Quality Control Software

birta

Bayesian Inference of Regulation of Transcriptional Activity

netbenchmark

Benchmarking of several gene network inference methods

paubellot/netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

markvdwiel/GRridge

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

GRridge

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

jardimViniciusC/BioNetStat

Biological Network Analysis

BioNetStat

Biological Network Analysis

almeidasilvaf/BioNERO

Biological Network Reconstruction Omnibus

gaggle

Broadcast data between R and Gaggle

guokai8/CandiHap

Build Haplotye and Generate Figures

huerqiang/prioGene

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

prioGene

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

CausalR

Causal network analysis methods

CHRONOS

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

redsnic/CIMICE

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

coexnet

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

juancholkovich/coexnet

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

jdhenaos/coexnet

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

gibbslab/coexnet

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

CEMiTool

Co-expression Modules identification Tool

csbl-usp/CEMiTool

Co-expression Modules identification Tool

Rvirgenslane/GmicR

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

GmicR

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

QuaternaryProd

Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

BiGGR

Constraint based modeling in R using metabolic reconstruction databases

hettling/BiGGR

Constraint based modeling in R using metabolic reconstruction databases

pmpsa-hpc/NPAModels

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

philipmorrisintl/NPAModels

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

anzezupanic/NPAmodels

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

RGraph2js

Convert a Graph into a D3js Script

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

RemyNicolle/CoRegNet-bioc

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

RemyNicolle/CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

RemyNicolle/CoRegNet-dev

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

COSNet

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

DART

Denoising Algorithm based on Relevance network Topology

balomenos/DEsubs

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

DEsubs

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

Wancen/airpart

Differential cell-type-specific allelic imbalance

dcanr

Differential co-expression/association network analysis

AlmaasLab/csdR

Differential gene co-expression

elisabettasciacca/DEGGs

Differentially Expressed Gene-Gene pairs

b2slab/diffusion

Diffusion scores on biological networks

b2slab/diffuStats

Diffusion scores on biological networks

diffuStats

Diffusion scores on biological networks

RCytoscape

Display and manipulate graphs in Cytoscape

tmuetze/Bioconductor_RCy3_the_new_RCytoscape

Display and manipulate graphs in Cytoscape >= 3.3.0

RCyjs

Display and manipulate graphs in cytoscape.js

paul-shannon/RCyjs

Display and manipulate graphs in cytoscape.js

PriceLab/RCyjs

Display and manipulate graphs in cytoscape.js

sysbiolab/TreeAndLeaf

Displaying binary trees with focus on dendrogram leaves

ddgraph

Distinguish direct and indirect interactions with Graphical Modelling

guokai8/microbial

Do 16s Data Analysis and Generate Figures

microbial

Do 16s Data Analysis and Generate Figures

hpages/ugraph

Efficient graph representation and manipulation in Bioconductor

hpages/graph4

Efficient graph representation and manipulation in Bioconductor

hpages/graph2

Efficient graph representation and manipulation in Bioconductor

malhamdoosh/EGSEA

Ensemble of Gene Set Enrichment Analyses

EGSEA

Ensemble of Gene Set Enrichment Analyses

apComplex

Estimate protein complex membership using AP-MS protein data

rcastelo/qpgraph

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

qpgraph

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

sarbal/EGAD

Extending guilt by association by degree

EGAD

Extending guilt by association by degree

csbl-usp/fcoex

FCBF-based Co-Expression Networks for Single Cells

lubianat/fcoex

FCBF-based Co-Expression Networks for Single Cells

fcoex

FCBF-based Co-Expression Networks for Single Cells

cbg-ethz/TiMEx

Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

AlmaasLab/micInt

Find microbial interactions

antagomir/netresponse

Functional Network Analysis

netresponse

Functional Network Analysis

cytoscape/r2cytoscape

Functions for Cytoscape Automation

cytoscape/RCy3

Functions to Access and Control Cytoscape

RCy3

Functions to Access and Control Cytoscape

maigesPack

Functions to handle cDNA microarray data, including several methods of data analysis

GeneNetworkBuilder

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

jianhong/GeneNetworkBuilder

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

aertslab/GENIE3

GEne Network Inference with Ensemble of trees

GENIE3

GEne Network Inference with Ensemble of trees

gramm4R

Generalized correlation analysis and model construction strategy for metabolome and microbiome

chentianlu/gramm4R

Generalized correlation analysis and model construction strategy for metabolome and microbiome

wind22zhu/BioMedR

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

BioMedR

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

BioMedR

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

GRENITS

Gene Regulatory Network Inference Using Time Series

gsean

Gene Set Enrichment Analysis with Networks

dongminjung/gsean

Gene Set Enrichment Analysis with Networks

Bioconductor/GSEABase

Gene set enrichment data structures and methods

GSEABase

Gene set enrichment data structures and methods

Rgin

gin in R

hclimente/Rgin

gin in R

alexsanchezpla/goProfiles

goProfiles: an R package for the statistical analysis of functional profiles

goProfiles

goProfiles: an R package for the statistical analysis of functional profiles

chrarnold/GRaNIE

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

GraphAlignment

GraphAlignment

Bioconductor/graph

graph: A package to handle graph data structures

graph

graph: A package to handle graph data structures

vjcitn/graph

graph: A package to handle graph data structures

biocGraph

Graph examples and use cases in Bioinformatics

graphite

GRAPH Interaction from pathway Topological Environment

sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

keggorthology

graph support for KO, KEGG Orthology

GraphAT

Graph Theoretic Association Tests

martini

GWAS Incorporating Networks

hclimente/martini

GWAS Incorporating Networks

rHVDM

Hidden Variable Dynamic Modeling

fspetale/fgga

Hierarchical ensemble method based on factor graph

hipathia

HiPathia: High-throughput Pathway Analysis

martahidalgo/hipathia

HiPathia: High-throughput Pathway Analysis

babelomics/hipathia

HiPathia: High-throughput Pathway Analysis

rTRM

Identification of transcriptional regulatory modules from PPI networks

almeidasilvaf/syntenet

Inference And Analysis Of Synteny Networks

cellTree

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

predictionet

Inference for predictive networks designed for (but not limited to) genomic data

Luisiglm/KBoost

Inference of gene regulatory networks from gene expression data

dongminjung/PPInfer

Inferring functionally related proteins using protein interaction networks

PPInfer

Inferring functionally related proteins using protein interaction networks

Pigengene

Infers biological signatures from gene expression data

ScISI

In Silico Interactome

mirIntegrator

Integrating microRNA expression into signaling pathways for pathway analysis

LucaAnholt/PanViz

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

ibh

Interaction Based Homogeneity for Evaluating Gene Lists

RedeR

Interactive visualization and manipulation of nested networks

reactome/ReactomeGraph4R

Interface for the Reactome Graph Database

IMMAN

Interlog protein network reconstruction by Mapping and Mining ANalysis

jafarilab/IMMAN

Interlog protein network reconstruction by Mapping and Mining ANalysis

b2slab/FELLA

Interpretation and enrichment for metabolomics data

FELLA

Interpretation and enrichment for metabolomics data

joda

JODA algorithm for quantifying gene deregulation using knowledge

cbg-ethz/pathTiMEx

Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

KEGGgraph

KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Accio/KEGGgraph

KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Pi

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

Pi

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

MPIIComputationalEpigenetics/MAGAR

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

afukushima/MSEAp

Metabolite Set Enrichment Analysis (MSEA)

MetaboSignal

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

thomasp85/FindMyFriends

Microbial Comparative Genomics in R

FindMyFriends

Microbial Comparative Genomics in R

dschlauch/MONSTER

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

QuackenbushLab/MONSTER

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

MVCClass

Model-View-Controller (MVC) Classes

BioMVCClass

Model-View-Controller (MVC) Classes That Use Biobase

elvanov/MOGAMUN

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

MOGAMUN

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

almeidasilvaf/magrene

Motif Analysis In Gene Regulatory Networks

abodein/netOmics

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

paircompviz

Multiple comparison test visualization

johnrstevens/mvGST

Multivariate and directional gene set testing

mvGST

Multivariate and directional gene set testing

CORREP

Multivariate Correlation Estimator and Statistical Inference Procedures.

minet

Mutual Information NETworks

NeighborNet

Neighbor_net analysis

mil2041/netboxr

netboxr

netboxr

netboxr

ahmohamed/NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

aiminy/NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

netboost

Network Analysis Supported by Boosting

JiantaoShi/NetGPA

Network-based Gene Prioritization Analysis (NetGPA)

JiantaoShi/NetORA

Network-based pathway over-representation analysis (NetORA)

glmSparseNet

Network Centrality Metrics for Elastic-Net Regularized Models

sysbiomed/glmSparseNet

Network Centrality Metrics for Elastic-Net Regularized Models

pmpsa-hpc/NPA

Network Perturbation Amplitude

philipmorrisintl/NPA

Network Perturbation Amplitude

netReg

Network-Regularized Regression Models

BIMSBbioinfo/netSmooth

Network smoothing for scRNAseq

netSmooth

Network smoothing for scRNAseq

OmnipathR

OmniPath web service client

saezlab/OmnipathR

OmniPath web service client and more

chemokine/OmicsSBGN

Overlay omics data onto SBGN pathway diagram

pkgDepTools

Package Dependency Tools

Bioconductor/pkgDepTools

Package Dependency Tools

Ghoshlab/pairkat

PaIRKAT

singha53/pandaR

PANDA Algorithm

QuackenbushLab/pandaR

PANDA Algorithm

jnpaulson/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

mani2012/PathoStat

PathoStat Statistical Microbiome Analysis Package

PathoStat

PathoStat Statistical Microbiome Analysis Package

kpj/dce

Pathway Enrichment Based on Differential Causal Effects

cbg-ethz/dce

Pathway Enrichment Based on Differential Causal Effects

cbg-ethz/pareg

Pathway enrichment using a regularized regression approach

NCIgraph

Pathways from the NCI Pathways Database

paxtoolsr

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

Ilarius/metaDEA

Perform co-DE gene analysis

bozdaglab/PhenoGeneRanker

PhenoGeneRanker: A gene and phenotype prioritization tool

krumsiek/MoDentify

Phenotype-driven module identification

krumsieklab/MoDentify

Phenotype-driven module identification

PCpheno

Phenotypes and cellular organizational units

GWENA

Pipeline for augmented co-expression analysis

Kumquatum/GWENA

Pipeline for augmented co-expression analysis

PANR

Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

PoTRA-Package/PoTRA

PoTRA: Pathways of Topological Rank Analysis

PoTRA-Package/Development

PoTRA: Pathways of Topological Rank Analysis

PoTRA

PoTRA: Pathways of Topological Rank Analysis

ProCoNA

Protein co-expression network analysis (ProCoNA).

dongminjung/DeepPINCS

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

ppiStats

Protein-Protein Interaction Statistical Package

Bioconductor/ppiStats

Protein-Protein Interaction Statistical Package

paul-shannon/PSICQUIC

Proteomics Standard Initiative Common QUery InterfaCe

PSICQUIC

Proteomics Standard Initiative Common QUery InterfaCe

Rgraphviz

Provides plotting capabilities for R graph objects

kasperdanielhansen/Rgraphviz

Provides plotting capabilities for R graph objects

RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

alberto-valdeolivas/RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

sap01/TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

bd2kccd/r-causal

R-Causal Library

jingeyu/CSSN

Recovering spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data.

selcenari/ceRNAnetsim

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

ceRNAnetsim

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

pathRender

Render molecular pathways

waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

GSEABenchmarkeR

Reproducible GSEA Benchmarking

assaron/BioNet

Routines for the functional analysis of biological networks

BioNet

Routines for the functional analysis of biological networks

sincell

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

rsbml

R support for SBML, using libsbml

RTN

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

wikipathways/rWikiPathways

rWikiPathways - R client library for the WikiPathways API

egonw/rwikipathways

rWikiPathways - R client library for the WikiPathways API

egonw/rWikiPathways

rWikiPathways - R client library for the WikiPathways API

rWikiPathways

rWikiPathways - R client library for the WikiPathways API

datapplab/SBGNview

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

SBGNview

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

mdnestor/SBMLR

SBML-R Interface and Analysis Tools

SBMLR

SBML-R Interface and Analysis Tools

EnrichmentBrowser

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

lgeistlinger/EnrichmentBrowser

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

plotGrouper

Shiny app GUI wrapper for ggplot with built-in statistical analysis

jdgagnon/plotGrouper

Shiny app GUI wrapper for ggplot with built-in statistical analysis

SPIA

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

rScudo

Signature-based Clustering for Diagnostic Purposes

Matteo-Ciciani/rScudo

Signature-based Clustering for Diagnostic Purposes

Matteo-Ciciani/scudo

Signature-based Clustering for Diagnostic Purposes

signet

signet: Selection Inference in Gene NETworks

CMPG/signet

signet: Selection Inference in Gene NETworks

tallulandrews/scTarNet

Single-cell Targetted Network Inference

jianhaizhang/spatialHeatmap

spatialHeatmap

spatialHeatmap

spatialHeatmap

hansenlab/spqn

Spatial quantile normalization

spqn

Spatial quantile normalization

pablof1988/goSorensen

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

RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

csgroen/RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

SLGI

Synthetic Lethal Genetic Interaction

mccallm/ternarynet

Ternary Network Estimation

ternarynet

Ternary Network Estimation

splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

ZytoHMGU/splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

pcastellanoescuder/fobibsa

Tools For Manipulating FOBI Ontology

pcastellanoescuder/fobitools

Tools For Manipulating FOBI Ontology

pcastellanoescuder/FOBIEnrichR

Tools For Manipulating FOBI Ontology

Bioconductor/GOstats

Tools for manipulating GO and microarrays

GOstats

Tools for manipulating GO and microarrays

lgeistlinger/ToPASeq

Topology-based pathway analysis of RNA-seq data

ToPASeq

Topology-based pathway analysis of RNA-seq data

arthurvinx/transcriptogramer

Transcriptional analysis based on transcriptograms

transcriptogramer

Transcriptional analysis based on transcriptograms

ubioinformat/TraRe

Transcriptional Rewiring

enrichTF

Transcription Factors Enrichment Analysis

wzthu/enrichTF

Transcription Factors Enrichment Analysis

BIMIB-DISCo/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

TRONCO

TRONCO, an R package for TRanslational ONCOlogy

DEGraph

Two-sample tests on a graph

netZoo/netZooR

Unified methods for the inference and analysis of gene regulatory networks

superOmics/sparsenetgls

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

sparsenetgls

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

KEGGlincs

Visualize all edges within a KEGG pathway and overlay LINCS data

shanawhite-UC/KEGGlincs

Visualize all edges within a KEGG pathway and overlay LINCS data

uc-bd2k/KEGGlincs

Visualize all edges within a KEGG pathway and overlay LINCS data [option]

hyperdraw

Visualizing Hypergaphs

AnaGalhoz37/wppi

Weighting protein-protein interactions

LiNk-NY/package

What the Package Does (One Line, Title Case)

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