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

Bioconductor-mirror/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

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'.

chagasVinicius/RTNduals

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

RTNduals

Analysis of co-regulatory network motifs and inference of 'dual regulons'

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor-mirror/birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Bioconductor-mirror/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

wmchad/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Bioconductor-mirror/netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

gibbslab/coexnet

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

Bioconductor-mirror/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

CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

RemyNicolle/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

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

Bioconductor-mirror/apComplex

Estimate protein complex membership using AP-MS protein data

apComplex

Estimate protein complex membership using AP-MS protein data

Bioconductor-mirror/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

PriceLab/TReNA

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

aertslab/GENIE3

GEne Network Inference with Ensemble of trees

Bioconductor-mirror/GRENITS

Gene Regulatory Network Inference Using Time Series

GRENITS

Gene Regulatory Network Inference Using Time Series

rHVDM

Hidden Variable Dynamic Modeling

Bioconductor-mirror/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

Pigengene

Infers biological signatures from gene expression data

Bioconductor-mirror/Pigengene

Infers biological signatures from gene expression data

Bioconductor-mirror/ScISI

In Silico Interactome

ScISI

In Silico Interactome

CNORfeeder

Integration of CellNOptR to add missing links

Bioconductor-mirror/CNORfeeder

Integration of CellNOptR to add missing links

Bioconductor-mirror/joda

JODA algorithm for quantifying gene deregulation using knowledge

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

tongyin9002/MICMIC

Methylation regulation network inference with Conditional Mutual information based PC-algorithem

dschlauch/MONSTER

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

QuackenbushLab/MONSTER

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

minet

Mutual Information NETworks

Bioconductor-mirror/minet

Mutual Information NETworks

singha53/pandaR

PANDA Algorithm

Bioconductor-mirror/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

QuackenbushLab/pandaR

PANDA Algorithm

Bioconductor-mirror/PANR

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

PANR

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

Bioconductor-mirror/Path2PPI

Prediction of pathway-related protein-protein interaction networks

Path2PPI

Prediction of pathway-related protein-protein interaction networks

Bioconductor-mirror/ppiStats

Protein-Protein Interaction Statistical Package

ppiStats

Protein-Protein Interaction Statistical Package

MTZimmer/RITAN

Rapid Integration of Term Annotation and Network resources

Bioconductor-mirror/RITAN

Rapid Integration of Term Annotation and Network resources

RITAN

Rapid Integration of Term Annotation and Network resources

RTN

Reconstruction of transcriptional networks and analysis of master regulators

Bioconductor-mirror/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

SPEM

S-system parameter estimation method

Bioconductor-mirror/SPEM

S-system parameter estimation method

Bioconductor-mirror/RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

csgroen/RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

grndata

Synthetic Expression Data for Gene Regulatory Network Inference

Bioconductor-mirror/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/splineTCDiffExpr

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

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

uc-bd2k/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]

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]

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