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

Bioconductor-mirror/R3CPET

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

RTNduals

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

chagasVinicius/RTNmotifs

analysis of co-regulatory network motifs 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'.

Bioconductor-mirror/birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

wmchad/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Bioconductor-mirror/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

netbenchmark

Benchmarking of several gene network inference methods

Bioconductor-mirror/netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

paubellot/netbenchmark

Benchmarking of several gene network inference methods

jardimViniciusC/BioNetStat

Biological Network Analysis

BioNetStat

Biological Network Analysis

Bioconductor-mirror/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

juancholkovich/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

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Bioconductor-mirror/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

Bioconductor-mirror/miRLAB

Dry lab for exploring miRNA-mRNA relationships

miRLAB

Dry lab for exploring miRNA-mRNA relationships

nem

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Bioconductor-mirror/nem

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

cbg-ethz/epiNEM

epiNEM

Bioconductor-mirror/epiNEM

epiNEM

epiNEM

epiNEM

FRGEpistasis

Epistasis Analysis for Quantitative Traits by Functional Regression Model

Bioconductor-mirror/FRGEpistasis

Epistasis Analysis for Quantitative Traits by Functional Regression Model

apComplex

Estimate protein complex membership using AP-MS protein data

Bioconductor-mirror/apComplex

Estimate protein complex membership using AP-MS protein data

qpgraph

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

Bioconductor-mirror/qpgraph

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

rcastelo/qpgraph

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

TReNA

Fit transcriptional regulatory networks using gene expression, priors, machine learning

PriceLab/trena

Fit transcriptional regulatory networks using gene expression, priors, machine learning

PriceLab/trena-until-01mar2018

Fit transcriptional regulatory networks using gene expression, priors, machine learning

trena

Fit transcriptional regulatory networks using gene expression, priors, machine learning

PriceLab/TReNA

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Jialab-UCR/GDCRNATools

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

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

GRENITS

Gene Regulatory Network Inference Using Time Series

Bioconductor-mirror/GRENITS

Gene Regulatory Network Inference Using Time Series

Bioconductor-mirror/rHVDM

Hidden Variable Dynamic Modeling

rHVDM

Hidden Variable Dynamic Modeling

predictionet

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

Bioconductor-mirror/predictionet

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

Bioconductor-mirror/Pigengene

Infers biological signatures from gene expression data

Pigengene

Infers biological signatures from gene expression data

Bioconductor-mirror/ScISI

In Silico Interactome

ScISI

In Silico Interactome

Bioconductor-mirror/CNORfeeder

Integration of CellNOptR to add missing links

CNORfeeder

Integration of CellNOptR to add missing links

saezlab/CNORfeeder

Integration of CellNOptR to add missing links

joda

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor-mirror/joda

JODA algorithm for quantifying gene deregulation using knowledge

lpNet

Linear Programming Model for Network Inference

Bioconductor-mirror/lpNet

Linear Programming Model for Network Inference

cbg-ethz/mnem

Mixture Nested Effects Models

dschlauch/MONSTER

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

QuackenbushLab/MONSTER

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

Bioconductor-mirror/minet

Mutual Information NETworks

minet

Mutual Information NETworks

Bioconductor-mirror/pandaR

PANDA Algorithm

QuackenbushLab/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

singha53/pandaR

PANDA Algorithm

PANR

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

Bioconductor-mirror/PANR

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

Path2PPI

Prediction of pathway-related protein-protein interaction networks

Bioconductor-mirror/Path2PPI

Prediction of pathway-related protein-protein interaction networks

cbg-ethz/pcNEM

Probabilistic combinatorial nested effects model

Bioconductor-mirror/ppiStats

Protein-Protein Interaction Statistical Package

ppiStats

Protein-Protein Interaction Statistical Package

Bioconductor/ppiStats

Protein-Protein Interaction Statistical Package

RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

alberto-valdeolivas/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

Bioconductor-mirror/RITAN

Rapid Integration of Term Annotation and Network resources

Bioconductor-mirror/RTN

Reconstruction of transcriptional networks and analysis of master regulators

RTN

Reconstruction of transcriptional networks and analysis of master regulators

networkBMA

Regression-based network inference using Bayesian Model Averaging

Bioconductor-mirror/networkBMA

Regression-based network inference using Bayesian Model Averaging

SPONGE

Sparse Partial Correlations On Gene Expression

mlist/SPONGE

Sparse Partial Correlations On Gene Expression

SPEM

S-system parameter estimation method

Bioconductor-mirror/SPEM

S-system parameter estimation method

csgroen/RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

Bioconductor-mirror/RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

grndata

Synthetic Expression Data for Gene Regulatory Network Inference

YC3/SEPIRA

Systems EPigenomics Inference of Regulatory Activity

SEPIRA

Systems EPigenomics Inference of Regulatory Activity

ZytoHMGU/splineTimeR

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

splineTimeR

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

Bioconductor-mirror/splineTimeR

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

Bioconductor-mirror/splineTCDiffExpr

MartinFXP/B-NEM

training of logical models from indirect measurements of perturbation experiments

Bioconductor-mirror/tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

TRONCO

TRONCO, an R package for TRanslational ONCOlogy

BIMIB-DISCo/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

Bioconductor-mirror/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

shanawhite-UC/KEGGlincs

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

Bioconductor-mirror/KEGGlincs

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

KEGGlincs

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

uc-bd2k/KEGGlincs

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

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