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

saezlab/CARNIVAL

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

saezlab/CARNIVAL-Bioconductor-Dev

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

CARNIVAL

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

AMOUNTAIN

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

fairmiracle/AMOUNTAIN

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

SQUADD

Add-on of the SQUAD Software

CNORfuzzy

Addon to CellNOptR: Fuzzy Logic

saezlab/CNORfuzzy

Addon to CellNOptR: Fuzzy Logic

ANF

Affinity Network Fusion for Complex Patient Clustering

BeautyOfWeb/ANF

Affinity Network Fusion for Complex Patient Clustering

netprioR

A model for network-based prioritisation of genes

cbg-ethz/netprioR

A model for network-based prioritisation of genes

sysbiolab/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

cx30/INDEED

An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

RBGL

An interface to the BOOST graph library

osenan/cliqueMS

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

cliqueMS

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

lgeistlinger/PathNet

An R package for pathway analysis using topological information

PathNet

An R package for pathway analysis using topological information

QUBIC

An R package for qualitative biclustering in support of gene co-expression analyses

PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis

SCCC-BBC/PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

netbiov

A package for visualizing complex biological network

rTRMui

A shiny user interface for rTRM

nachoryu/ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

azampvd/DrugDiseaseNet

A Systems Biology Approach for Drug Repurposing

JhuangLab/CytoTree

A Toolkit for Flow And Mass Cytometry Data

flowSpy

A Toolkit for Flow And Mass Cytometry Data

JhuangLab/flowSpy

A Toolkit for Flow And Mass Cytometry Data

LiNk-NY/interactiveDisplaybase

Base package for enabling powerful shiny web displays of Bioconductor objects

interactiveDisplayBase

Base package for enabling powerful shiny web displays of Bioconductor objects

LiNk-NY/interactiveDisplayBase

Base package for enabling powerful shiny web displays of Bioconductor objects

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

wmchad/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

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

mpru/BIMEGA

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

torongs82/Bioc2019PanCancerStudy

Bioc2019PanCancerStudy

BioNetStat

Biological Network Analysis

jardimViniciusC/BioNetStat

Biological Network Analysis

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

SCA-IRCM/SingleCellSignalR

Cell Signalling Using Single Cell RNAseq Data Analysis

SingleCellSignalR

Cell Signalling Using Single Cell RNAseq Data Analysis

mil2041/CNCDriver

CNCDriver

gibbslab/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

coexnet

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

cbiagii/pcitRif

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

cbiagii/ceTF

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

CeTF

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

cbiagii/CeTF

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)

broadinstitute/CommunityAMARETTO

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

mil2041/CompositeDriver

CompositeDriver

hettling/BiGGR

Constraint based modeling in R using metabolic reconstruction databases

BiGGR

Constraint based modeling in R using metabolic reconstruction databases

GNET2

Constructing gene regulatory networks from expression data through functional module inference

chrischen1/GNET2

Constructing gene regulatory networks from expression data through functional module inference

jianlin-cheng/GNET2

Constructing gene regulatory networks from expression data through functional module inference

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

i3bionet/CoRegFlux

CoRegFlux

CoRegFlux

CoRegFlux

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

RemyNicolle/CoRegNet-dev

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

RemyNicolle/CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

COSNet

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

ecell/transomics2cytoscape

Create 3D transomics network view with Ã‡ytoscape and Cy3D

DeMAND

DeMAND

DEsubs

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

balomenos/DEsubs

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

dcanr

Differential co-expression/association network analysis

b2slab/diffusion

Diffusion scores on biological networks

diffuStats

Diffusion scores on biological networks

b2slab/diffuStats

Diffusion scores on biological networks

tmuetze/Bioconductor_RCy3_the_new_RCytoscape

Display and manipulate graphs in Cytoscape >= 3.3.0

DriverNet

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

miRLAB

Dry lab for exploring miRNA-mRNA relationships

malhamdoosh/EGSEA

Ensemble of Gene Set Enrichment Analyses

EGSEA

Ensemble of Gene Set Enrichment Analyses

cbg-ethz/epiNEM

epiNEM

epiNEM

epiNEM

sarbal/EGAD

Extending guilt by association by degree

EGAD

Extending guilt by association by degree

lubianat/fcoex

FCBF-based Co-Expression Networks for Single Cells

fcoex

FCBF-based Co-Expression Networks for Single Cells

csbl-usp/fcoex

FCBF-based Co-Expression Networks for Single Cells

FGNet

Functional Gene Networks derived from biological enrichment analyses

antagomir/netresponse

Functional Network Analysis

netresponse

Functional Network Analysis

llrs/BioCor

Functional similarities

BioCor

Functional similarities

cytoscape/r2cytoscape

Functions for Cytoscape Automation

RCy3

Functions to Access and Control Cytoscape

cytoscape/RCy3

Functions to Access and Control Cytoscape

GDCRNATools

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

Jialab-UCR/GDCRNATools

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

GENIE3

GEne Network Inference with Ensemble of trees

aertslab/GENIE3

GEne Network Inference with Ensemble of trees

WTaoUMC/RegEnrich

Gene regulator enrichment analysis

GRENITS

Gene Regulatory Network Inference Using Time Series

gsean

Gene Set Enrichment Analysis with Networks

dongminjung/gsean

Gene Set Enrichment Analysis with Networks

RGMQL

GenoMetric Query Language for R/Bioconductor

DEIB-GECO/RGMQL

GenoMetric Query Language for R/Bioconductor

hclimente/Rgin

gin in R

Rgin

gin in R

GuangchuangYu/GOSemSim

GO-terms Semantic Similarity Measures

GOSemSim

GO-terms Semantic Similarity Measures

GraphAlignment

GraphAlignment

sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

graphite

GRAPH Interaction from pathway Topological Environment

GraphAT

Graph Theoretic Association Tests

hclimente/martini

GWAS Incorporating Networks

martini

GWAS Incorporating Networks

BiRewire

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)

rTRM

Identification of transcriptional regulatory modules from PPI networks

MoonlightR

Identify oncogenes and tumor suppressor genes from omics data

ibsquare/MoonlightR

Identify oncogenes and tumor suppressor genes from omics data

broadinstitute/ImagingAMARETTO

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

OmnipathR

Import Omnipath network

saezlab/OmnipathR

Import Omnipath network

PPInfer

Inferring functionally related proteins using protein interaction networks

dongminjung/PPInfer

Inferring functionally related proteins using protein interaction networks

tnaake/MetNet

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

MetNet

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

cbg-ethz/nempi

Inferring unobserved perturbations from gene expression data

Pigengene

Infers biological signatures from gene expression data

mirIntegrator

Integrating microRNA expression into signaling pathways for pathway analysis

PengNi/dSimer

Integration of Disease Similarity Methods

dSimer

Integration of Disease Similarity Methods

bioCancer

Interactive Multi-Omics Cancers Data Visualization and Analysis

kmezhoud/bioCancer

Interactive Multi-Omics Cancers Data Visualization and Analysis

RedeR

Interactive visualization and manipulation of nested networks

jafarilab/IMMAN

Interlog protein network reconstruction by Mapping and Mining ANalysis

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

awaardenberg/KinSwingR

KinSwingR: network-based kinase activity prediction

KinSwingR

KinSwingR: network-based kinase activity prediction

levi

Landscape Expression Visualization Interface

jrybarczyk/levi

Landscape Expression Visualization Interface

ChenWeiyan/LandSCENT

Landscape Single Cell Entropy

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

Linnorm

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

LiquidAssociation

LiquidAssociation

afukushima/MSEAp

Metabolite Set Enrichment Analysis (MSEA)

MetaboSignal

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

TxRegInfra

Metadata management for multiomic specification of transcriptional regulatory networks

vjcitn/TxRegInfra

Metadata management for multiomic specification of transcriptional regulatory networks

gevaertlab/MethylMix

MethylMix: Identifying methylation driven cancer genes

gevaertlab/methylmix

MethylMix: Identifying methylation driven cancer genes

MethylMix

MethylMix: Identifying methylation driven cancer genes

Krutik6/TimiRGeN

microRNA-mRNA Integration, Analysis and Network Generation Tool

mnem

Mixture Nested Effects Models

cbg-ethz/mnem

Mixture Nested Effects Models

fairmiracle/MODA

MODA: MOdule Differential Analysis for weighted gene co-expression network

MODA

MODA: MOdule Differential Analysis for weighted gene co-expression network

lionessR

Modeling networks for individual samples using LIONESS

QuackenbushLab/MONSTER

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

dschlauch/MONSTER

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

califano-lab/MOMA

Multi Omic Master Regulator Analysis

MOMA

Multi Omic Master Regulator Analysis

langholee/XINA

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

XINA

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

minet

Mutual Information NETworks

ndexr

NDEx R client library

frankkramer-lab/ndexr

NDEx R client library

mil2041/netboxr

netboxr

netboxr

netboxr

aiminy/NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

ahmohamed/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)

netDx

Network-based patient classifier

BaderLab/netDx

Network-based patient classifier

ressomlab/MetID

Network-based prioritization of putative metabolite IDs

xw187/MetID

Network-based prioritization of putative metabolite IDs

MetID

Network-based prioritization of putative metabolite IDs

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

dirmeier/netReg

Network-Regularized Regression Models

NetSAM

Network Seriation And Modularization

netSmooth

Network smoothing for scRNAseq

BIMSBbioinfo/netSmooth

Network smoothing for scRNAseq

Onassis

OnASSIs Ontology Annotation and Semantic SImilarity software

eugeniaeueu/Onassis

OnASSIs Ontology Annotation and Semantic SImilarity software

oppti

Outlier Protein and Phosphosite Target Identifier

Huang-lab/oppti

Outlier Protein and Phosphosite Target Identifier

isglobal-brge/CTDquerier

Package for CTDbase data query, visualization and downstream analysis

CTDquerier

Package for CTDbase data query, visualization and downstream analysis

interactiveDisplay

Package for enabling powerful shiny web displays of Bioconductor objects

QuackenbushLab/pandaR

PANDA Algorithm

singha53/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

jnpaulson/pandaR

PANDA Algorithm

paxtoolsr

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

cannin/paxtoolsr

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

BioPAX/paxtoolsr

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

PCAN

Phenotype Consensus ANalysis (PCAN)

krumsiek/MoDentify

Phenotype-driven module identification

krumsieklab/MoDentify

Phenotype-driven module identification

PCpheno

Phenotypes and cellular organizational units

Kumquatum/GWENA

Pipeline for augmented co-expression analysis

PoTRA

PoTRA: Pathways of Topological Rank Analysis

PoTRA-Package/Development

PoTRA: Pathways of Topological Rank Analysis

PoTRA-Package/PoTRA

PoTRA: Pathways of Topological Rank Analysis

Path2PPI

Prediction of pathway-related protein-protein interaction networks

pcot2

Principal Coordinates and Hotelling's T-Square method

Bioconductor/ppiStats

Protein-Protein Interaction Statistical Package

ppiStats

Protein-Protein Interaction Statistical Package

pathifier

Quantify deregulation of pathways in cancer

alberto-valdeolivas/RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

MTZimmer/RITAN

Rapid Integration of Term Annotation and Network resources

RITAN

Rapid Integration of Term Annotation and Network resources

sap01/TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

rrvgo

Reduce + Visualize GO

ssayols/rrvgo

Reduce + Visualize GO

ssayols/rrvgo-ci

Reduce + Visualize GO

ssayols/RVGO

Reduce + Visualize GO

networkBMA

Regression-based network inference using Bayesian Model Averaging

selcenari/ceRNAnetsim

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

ceRNAnetsim

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

gevaertlab/AMARETTO

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

broadinstitute/PerturbationAMARETTO

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

AMARETTO

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

regutools

regutools: an R package for data extraction from RegulonDB

GSEABenchmarkeR

Reproducible GSEA Benchmarking

waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

BioNet

Routines for the functional analysis of biological networks

frankkramer-lab/RCX

R package implementing the Cytoscape Exchange (CX) format

rsbml

R support for SBML, using libsbml

RTN

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

egonw/rWikiPathways

rWikiPathways - R client library for the WikiPathways API

wikipathways/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

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

Matteo-Ciciani/scudo

Signature-based Clustering for Diagnostic Purposes

rScudo

Signature-based Clustering for Diagnostic Purposes

Matteo-Ciciani/rScudo

Signature-based Clustering for Diagnostic Purposes

GreallyLab/SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

AJEinstein/SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

WangNing0420/SCIRA

Single Cell Inference of Regulatory Activity

KechrisLab/SmCCNet

Sparse multiple canonical correlation network analysis tool

SmCCNet

Sparse Multiple Canonical Correlation Network Analysis Tool

SANTA

Spatial Analysis of Network Associations

SpidermiR

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

claudiacava/SpidermiR

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

SPEM

S-system parameter estimation method

StarBioTrek

StarBioTrek

claudiacava/StarBioTrek

StarBioTrek

claudiacava/StarTrek

StarBioTrek

cbg-ethz/knockdown

Statistical Analysis of High-Throughput Genetic Perturbation Screens

dirmeier/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

STRINGdb

STRINGdb (Search Tool for the Retrieval of Interacting proteins database)

grndata

Synthetic Expression Data for Gene Regulatory Network Inference

SLGI

Synthetic Lethal Genetic Interaction

SEPIRA

Systems EPigenomics Inference of Regulatory Activity

YC3/SEPIRA

Systems EPigenomics Inference of Regulatory Activity

TCGAbiolinks

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

BioinformaticsFMRP/TCGAbiolinks

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

BioinformaticsFMRP/TCGAbiolinksGUI

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

TCGAbiolinksGUI

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

PROFANCY

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

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

saezlab/CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

MartinFXP/B-NEM

training of logical models from indirect measurements of perturbation experiments

arthurvinx/transcriptogramer

Transcriptional analysis based on transcriptograms

transcriptogramer

Transcriptional analysis based on transcriptograms

Mengbo-Li/brainClass

Transcriptional Data Guided fMRI Network Classification

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

vtpnet

variant-transcription factor-phenotype networks

caOmicsV

Visualization of multi-dimentional cancer genomics data

hzhanghenry/caOmicsV

Visualization of multi-dimentional cancer genomics data

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]

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