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

RTNduals

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

chagasVinicius/RTNduals-alpha

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/RTNmotifs

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

cliqueMS

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

osenan/cliqueMS

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

nachoryu/ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

JhuangLab/CytoTree

A Toolkit for Flow And Mass Cytometry Data

JhuangLab/flowSpy

A Toolkit for Flow And Mass Cytometry Data

flowSpy

A Toolkit for Flow And Mass Cytometry Data

CytoTree

A Toolkit for Flow And Mass Cytometry Data

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

wmchad/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

paubellot/netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

netbenchmark

Benchmarking of several gene network inference methods

jardimViniciusC/BioNetStat

Biological Network Analysis

BioNetStat

Biological Network Analysis

almeidasilvaf/BioNERO

Biological Network Reconstruction Omnibus

ywhsiao/ceRNAR

ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

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

gibbslab/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

GmicR

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

Rvirgenslane/GmicR

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

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

chrischen1/GNET2

Constructing gene regulatory networks from expression data through functional module inference

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

RemyNicolle/CoRegNet-bioc

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

dcanr

Differential co-expression/association network analysis

elisabettasciacca/DEGGs

Differentially Expressed Gene-Gene pairs

miRLAB

Dry lab for exploring miRNA-mRNA relationships

nem

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

cbg-ethz/epiNEM

epiNEM

epiNEM

epiNEM

FRGEpistasis

Epistasis Analysis for Quantitative Traits by Functional Regression Model

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

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

netresponse

Functional Network Analysis

antagomir/netresponse

Functional Network Analysis

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

aertslab/GENIE3

GEne Network Inference with Ensemble of trees

GENIE3

GEne Network Inference with Ensemble of trees

RegEnrich

Gene regulator enrichment analysis

WTaoUMC/RegEnrich

Gene regulator enrichment analysis

GRENITS

Gene Regulatory Network Inference Using Time Series

ytakemon/GINIR

Genetic inteRaction and EssenTiality neTwork mApper

chrarnold/GRaNIE

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

rHVDM

Hidden Variable Dynamic Modeling

fspetale/fgga

Hierarchical ensemble method based on factor graph

mrbakhsh/HPiP

Host-Pathogen Interaction Prediction

sankaranlab/SCAVENGE

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

almeidasilvaf/syntenet

Inference And Analysis Of Synteny Networks

predictionet

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

Luisiglm/KBoost

Inference of gene regulatory networks from gene expression data

cbg-ethz/nempi

Inferring unobserved perturbations from gene expression data

Pigengene

Infers biological signatures from gene expression data

ScISI

In Silico Interactome

saezlab/CellNOpt-Feeder

Integration of CellNOptR to add missing links

saezlab/CNORfeeder

Integration of CellNOptR to add missing links

CNORfeeder

Integration of CellNOptR to add missing links

joda

JODA algorithm for quantifying gene deregulation using knowledge

lpNet

Linear Programming Model for Network Inference

mnem

Mixture Nested Effects Models

cbg-ethz/mnem

Mixture Nested Effects Models

lionessR

Modeling networks for individual samples using LIONESS

dschlauch/MONSTER

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

QuackenbushLab/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

Fjeanneret/multiSight

Multi-omics Classification, Functional Enrichment and Network Inference analysis

abodein/netOmics

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

minet

Mutual Information NETworks

QuackenbushLab/pandaR

PANDA Algorithm

singha53/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

jnpaulson/pandaR

PANDA Algorithm

bozdaglab/PhenoGeneRanker

PhenoGeneRanker: A gene and phenotype prioritization tool

krumsiek/MoDentify

Phenotype-driven module identification

krumsieklab/MoDentify

Phenotype-driven module identification

noriakis/CBNplotTest

plot bayesian network inferred from gene expression data based on enrichment analysis results

noriakis/CBNplot

plot bayesian network inferred from gene expression data based on enrichment analysis results

PANR

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

fosterlab/PrInCE-R

Predicting Interactomes from Co-Elution

fosterlab/PrInCE

Predicting Interactomes from Co-Elution

PrInCE

Predicting Interactomes from Co-Elution

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

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

sap01/TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

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)

regutools

regutools: an R package for data extraction from RegulonDB

Informeasure

R implementation of Information measures

chupan1218/Informeasure

R implementation of informtion measures

RTN

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

WangNing0420/SCIRA

Single Cell Inference of Regulatory Activity

biomedbigdata/SPONGE

Sparse Partial Correlations On Gene Expression

SPONGE

Sparse Partial Correlations On Gene Expression

mlist/SPONGE

Sparse Partial Correlations On Gene Expression

hansenlab/spqn

Spatial quantile normalization

spqn

Spatial quantile normalization

SPEM

S-system parameter estimation method

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

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

MartinFXP/B-NEM

Training of logical models from indirect measurements of perturbation experiments

MartinFXP/bnem

Training of logical models from indirect measurements of perturbation experiments

Mengbo-Li/brainClass

Transcriptional Data Guided fMRI Network Classification

ahonkela/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

netZoo/netZooR

Unified methods for the inference and analysis of gene regulatory networks

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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