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

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)

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

paubellot/netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

jardimViniciusC/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

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

RemyNicolle/CoRegNet-dev

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

miRLAB

Dry lab for exploring miRNA-mRNA relationships

Bioconductor-mirror/miRLAB

Dry lab for exploring miRNA-mRNA relationships

Bioconductor-mirror/nem

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

nem

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

Bioconductor-mirror/epiNEM

epiNEM

epiNEM

epiNEM

cbg-ethz/epiNEM

epiNEM

Bioconductor-mirror/FRGEpistasis

Epistasis Analysis for Quantitative Traits by Functional Regression Model

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

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

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

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

GENIE3

GEne Network Inference with Ensemble of trees

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

Bioconductor-mirror/rHVDM

Hidden Variable Dynamic Modeling

rHVDM

Hidden Variable Dynamic Modeling

Bioconductor-mirror/predictionet

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

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

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

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

cbg-ethz/mnem

mnem

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

QuackenbushLab/pandaR

PANDA Algorithm

singha53/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

Bioconductor-mirror/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

Bioconductor-mirror/Path2PPI

Prediction of pathway-related protein-protein interaction networks

Path2PPI

Prediction of pathway-related protein-protein interaction networks

cbg-ethz/pcNEM

Probabilistic combinatorial nested effects model

ppiStats

Protein-Protein Interaction Statistical Package

Bioconductor/ppiStats

Protein-Protein Interaction Statistical Package

Bioconductor-mirror/ppiStats

Protein-Protein Interaction Statistical Package

alberto-valdeolivas/RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks

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

Bioconductor-mirror/networkBMA

Regression-based network inference using Bayesian Model Averaging

networkBMA

Regression-based network inference using Bayesian Model Averaging

SPONGE

Sparse Partial Correlations On Gene Expression

mlist/SPONGE

Sparse Partial Correlations On Gene Expression

Bioconductor-mirror/SPEM

S-system parameter estimation method

SPEM

S-system parameter estimation method

RTNsurvival

Survival analysis using transcriptional networks inferred by the RTN package

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

YC3/SEPIRA

Systems EPigenomics Inference of Regulatory Activity

Bioconductor-mirror/splineTCDiffExpr

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

splineTimeR

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

Bioconductor-mirror/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

BIMIB-DISCo/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

TRONCO

TRONCO, an R package for TRanslational ONCOlogy

shanawhite-UC/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]

Bioconductor-mirror/KEGGlincs

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

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