sirusb/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

R3CPET

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

CARNIVAL

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

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

cannin/paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

BioPAX/paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

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

anacarolinaleote/ADImpute

Adaptive Dropout Imputer (ADImpute)

ADImpute

Adaptive Dropout Imputer (ADImpute)

beyergroup/ADImpute

Adaptive Dropout Imputer (ADImpute)

SQUADD

Add-on of the SQUAD Software

saezlab/CNORfuzzy

Addon to CellNOptR: Fuzzy Logic

CNORfuzzy

Addon to CellNOptR: Fuzzy Logic

BeautyOfWeb/ANF

Affinity Network Fusion for Complex Patient Clustering

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

TreeAndLeaf

An alternative to dendrogram visualization and insertion of multiple layers of information

leonardokume/TreeAndLeaf

An alternative to dendrogram visualization and insertion of multiple layers of information

neurogenomics/HPOExplorer

Analysis and Visualisation of the Human Phenotype Ontology

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

PathNet

An R package for pathway analysis using topological information

lgeistlinger/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

ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

nachoryu/ASpediaFI

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

azampvd/DrugDiseaseNet

A Systems Biology Approach for Drug Repurposing

CytoTree

A Toolkit for Flow And Mass Cytometry Data

flowSpy

A Toolkit for Flow And Mass Cytometry Data

JhuangLab/CytoTree

A Toolkit for Flow And Mass Cytometry Data

JhuangLab/flowSpy

A Toolkit for Flow And Mass Cytometry Data

transomics2cytoscape

A tool set for 3D Trans-Omic network visualization with Cytoscape

ecell/transomics2cytoscape

A tool set for 3D Trans-Omic network visualization with Cytoscape

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)

wmchad/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

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

jardimViniciusC/BioNetStat

Biological Network Analysis

BioNetStat

Biological Network Analysis

almeidasilvaf/BioNERO

Biological Network Reconstruction Omnibus

almeidasilvaf/cageminer

Candidate Gene Miner

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

BASiNETEntropy

Classification of RNA Sequences using Complex Network and Information Theory

mil2041/CNCDriver

CNCDriver

jdhenaos/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

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

CeTF

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

cbiagii/pcitRif

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

cbiagii/ceTF

csbl-usp/CEMiTool

Co-expression Modules identification Tool

CEMiTool

Co-expression Modules identification Tool

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)

broadinstitute/CommunityAMARETTO

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

mil2041/CompositeDriver

CompositeDriver

boseb/CTDPathSim2.0

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

bozdaglab/CTDPathSim2.0

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

BiGGR

Constraint based modeling in R using metabolic reconstruction databases

hettling/BiGGR

Constraint based modeling in R using metabolic reconstruction databases

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

GNET2

Constructing gene regulatory networks from expression data through functional module inference

anzezupanic/NPAmodels

Contains utils for loading and manipulating two-layers structure network models

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

RGraph2js

Convert a Graph into a D3js Script

CoRegFlux

CoRegFlux

i3bionet/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-bioc

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

RemyNicolle/CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory
networks

saezlab/cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space)

saezlab/COSMOS

COSMOS (Causal Oriented Search of Multi-Omic Space)

COSNet

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

dendroNetwork

Create Networks of Dendrochronological Series using Pairwise Similarity

saezlab/decoupleR

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DeMAND

DeMAND

balomenos/DEsubs

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

DEsubs

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

dcanr

Differential co-expression/association network analysis

AlmaasLab/csdR

Differential gene co-expression

elisabettasciacca/DEGGs

Differentially Expressed Gene-Gene pairs

b2slab/diffuStats

Diffusion scores on biological networks

diffuStats

Diffusion scores on biological networks

b2slab/diffusion

Diffusion scores on biological networks

tmuetze/Bioconductor_RCy3_the_new_RCytoscape

Display and manipulate graphs in Cytoscape >= 3.3.0

sysbiolab/TreeAndLeaf

Displaying binary trees with focus on dendrogram leaves

DriverNet

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

miRLAB

Dry lab for exploring miRNA-mRNA relationships

TFactSR

Enrichment Approach to Predict Which Transcription Factors are Regulated

EGSEA

Ensemble of Gene Set Enrichment Analyses

malhamdoosh/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

fcoex

FCBF-based Co-Expression Networks for Single Cells

lubianat/fcoex

FCBF-based Co-Expression Networks for Single Cells

csbl-usp/fcoex

FCBF-based Co-Expression Networks for Single Cells

rosscm/fedupShiny

fedupShiny

ctlab/gatom

Finding an Active Metabolic Module in Atom Transition Network

rosscm/fedup

Fisher's Test for Enrichment and Depletion of User-Defined Pathways

rosscm/FEDUP

Fisher's Test for Enrichment and Depletion of User-Defined Pathways

adeschen/gprofiler2cytoscape

From functional enrichment results to biological networks

FGNet

Functional Gene Networks derived from biological enrichment analyses

netresponse

Functional Network Analysis

antagomir/netresponse

Functional Network Analysis

BioCor

Functional similarities

llrs/BioCor

Functional similarities

cytoscape/r2cytoscape

Functions for Cytoscape Automation

RCy3

Functions to Access and Control Cytoscape

cytoscape/RCy3

Functions to Access and Control Cytoscape

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

gsean

Gene Set Enrichment Analysis with Networks

dongminjung/gsean

Gene Set Enrichment Analysis with Networks

ytakemon/GINIR

Genetic inteRaction and EssenTiality neTwork mApper

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

YuLab-SMU/GOSemSim

GO-terms Semantic Similarity Measures

GOSemSim

GO-terms Semantic Similarity Measures

GuangchuangYu/GOSemSim

GO-terms Semantic Similarity Measures

GraphAlignment

GraphAlignment

graphite

GRAPH Interaction from pathway Topological Environment

sales-lab/graphite

GRAPH Interaction from pathway Topological Environment

GraphAT

Graph Theoretic Association Tests

martini

GWAS Incorporating Networks

hclimente/martini

GWAS Incorporating Networks

fspetale/fgga

Hierarchical ensemble method based on factor graph

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)

mrbakhsh/HPiP

Host-Pathogen Interaction Prediction

rTRM

Identification of transcriptional regulatory modules from PPI networks

fl-yu/SCAVENGE

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

sankaranlab/SCAVENGE

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

MoonlightR

Identify oncogenes and tumor suppressor genes from omics data

ELELAB/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

almeidasilvaf/syntenet

Inference And Analysis Of Synteny Networks

Luisiglm/KBoost

Inference of gene regulatory networks from gene expression data

dongminjung/PPInfer

Inferring functionally related proteins using protein interaction networks

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

LucaAnholt/PanViz

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

dSimer

Integration of Disease Similarity Methods

PengNi/dSimer

Integration of Disease Similarity Methods

anna-pacinkova/intomics_package

Integrative analysis of multi-omics data to infer regulatory networks

gongcongcong/mbOmic

Integrative analysis of the microbiome and metabolome

kmezhoud/bioCancer

Interactive Multi-Omics Cancers Data Visualization and Analysis

bioCancer

Interactive Multi-Omics Cancers Data Visualization and Analysis

RedeR

Interactive visualization and manipulation of nested networks

reactome/ReactomeGraph4R

Interface for the Reactome Graph Database

jafarilab/IMMAN

Interlog protein network reconstruction by Mapping and Mining ANalysis

IMMAN

Interlog protein network reconstruction by Mapping and Mining ANalysis

FELLA

Interpretation and enrichment for metabolomics data

b2slab/FELLA

Interpretation and enrichment for metabolomics data

jiang-junyao/IReNA

IReNA

KinSwingR

KinSwingR: network-based kinase activity prediction

awaardenberg/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)

michaelwitting/wormLipidPredictR

Lipid reaction prediction based on WormJam

LiquidAssociation

LiquidAssociation

MPIIComputationalEpigenetics/MAGAR

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

afukushima/MSEAp

Metabolite Set Enrichment Analysis (MSEA)

MetaboSignal

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

vjcitn/TxRegInfra

Metadata management for multiomic specification of transcriptional regulatory networks

TxRegInfra

Metadata management for multiomic specification of transcriptional regulatory networks

vjcitn/TxRegInfra2

Metadata management for multiomic specification of transcriptional regulatory networks, version 2

MethylMix

MethylMix: Identifying methylation driven cancer genes

gevaertlab/MethylMix

MethylMix: Identifying methylation driven cancer genes

gevaertlab/methylmix

MethylMix: Identifying methylation driven cancer genes

microbiome/miaSim

Microbiome Data Simulation

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)

elvanov/MOGAMUN

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

MOGAMUN

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

tdrose/mosbi

Molecular Signature identification using Biclustering

MOMA

Multi Omic Master Regulator Analysis

califano-lab/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

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

netboxr

netboxr

mil2041/netboxr

netboxr

aiminy/NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

ahmohamed/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)

BaderLab/netDx

Network-based patient classifier

netDx

Network-based patient classifier

MetID

Network-based prioritization of putative metabolite IDs

ressomlab/MetID

Network-based prioritization of putative metabolite IDs

xw187/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

philipmorrisintl/NPA

Network Perturbation Amplitude

pmpsa-hpc/NPA

Network Perturbation Amplitude

netReg

Network-Regularized Regression Models

NetSAM

Network Seriation And Modularization

BIMSBbioinfo/netSmooth

Network smoothing for scRNAseq

netSmooth

Network smoothing for scRNAseq

OmnipathR

OmniPath web service client

saezlab/OmnipathR

OmniPath web service client and more

eugeniaeueu/Onassis

OnASSIs Ontology Annotation and Semantic SImilarity software

Onassis

OnASSIs Ontology Annotation and Semantic SImilarity software

Huang-lab/oppti

Outlier Protein and Phosphosite Target Identifier

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

Ghoshlab/pairkat

PaIRKAT

jnpaulson/pandaR

PANDA Algorithm

singha53/pandaR

PANDA Algorithm

QuackenbushLab/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

cbg-ethz/dce

Pathway Enrichment Based on Differential Causal Effects

kpj/dce

Pathway Enrichment Based on Differential Causal Effects

cbg-ethz/pareg

Pathway enrichment using a regularized regression approach

paxtoolsr

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

Ilarius/metaDEA

Perform co-DE gene analysis

bozdaglab/PhenoGeneRanker

PhenoGeneRanker: A gene and phenotype prioritization tool

PCAN

Phenotype Consensus ANalysis (PCAN)

krumsiek/MoDentify

Phenotype-driven module identification

krumsieklab/MoDentify

Phenotype-driven module identification

PCpheno

Phenotypes and cellular organizational units

GWENA

Pipeline for augmented co-expression analysis

Kumquatum/GWENA

Pipeline for augmented co-expression analysis

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

PoTRA-Package/PoTRA

PoTRA: Pathways of Topological Rank Analysis

PoTRA-Package/Development

PoTRA: Pathways of Topological Rank Analysis

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

dongminjung/DeepPINCS

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

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

TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

sap01/TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

rrvgo

Reduce + Visualize GO

imbforge/rrvgo

Reduce + Visualize GO

ssayols/rrvgo-ci

Reduce + Visualize GO

ssayols/RVGO

Reduce + Visualize GO

ssayols/rrvgo

Reduce + Visualize GO

networkBMA

Regression-based network inference using Bayesian Model Averaging

ceRNAnetsim

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

selcenari/ceRNAnetsim

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

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

gevaertlab/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

waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

GSEABenchmarkeR

Reproducible GSEA Benchmarking

Informeasure

R implementation of Information measures

chupan1218/Informeasure

R implementation of informtion measures

assaron/BioNet

Routines for the functional analysis of biological networks

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

rWikiPathways

rWikiPathways - R client library for the WikiPathways API

egonw/rwikipathways

rWikiPathways - R client library for the WikiPathways API

wikipathways/rWikiPathways

rWikiPathways - R client library for the WikiPathways API

SBMLR

SBML-R Interface and Analysis Tools

mdnestor/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

AJEinstein/SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

GreallyLab/SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome

aet21/SCENT

Single Cell Entropy

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

alexjcornish/SANTA

Spatial Analysis of Network Associations

spatialHeatmap

spatialHeatmap

jianhaizhang/spatialHeatmap

spatialHeatmap

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

perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/knockdown

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

dirmeier/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

fritz616/STRINGdb_mod

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

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

almeidasilvaf/cogeqc

Systematic quality checks on comparative genomics analyses

YC3/SEPIRA

Systems EPigenomics Inference of Regulatory Activity

SEPIRA

Systems EPigenomics Inference of Regulatory Activity

BioinformaticsFMRP/TCGAbiolinks

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

daniel615212950/TCGAbiolinks

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

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"

pageRank

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

hd2326/pageRank

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

mccallm/ternarynet

Ternary Network Estimation

PROFANCY

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

Krutik6/TimiRGeN

Time sensitive microRNA-mRNA integration, analysis and network generation tool

TimiRGeN

Time sensitive microRNA-mRNA integration, analysis and network generation tool

saezlab/PHONEMeS

tool to run PHONEMeS on phosphoproteomic data

saezlab/CellNOptR

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

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

MartinFXP/bnem

Training of logical models from indirect measurements of perturbation experiments

transcriptogramer

Transcriptional analysis based on transcriptograms

arthurvinx/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

netZoo/netZooR

Unified methods for the inference and analysis of gene regulatory networks

b2slab/mWISE

Untargeted LC-MS data annotation

vtpnet

variant-transcription factor-phenotype networks

DavisLaboratory/enrichnets

Visualising Set Enrichment Analysis Results

DavisLaboratory/vissE

Visualising Set Enrichment Analysis Results

noriakis/wcGeneSummary

visualization and interpretation of textual information from omics summary data through network analysis

hzhanghenry/caOmicsV

Visualization of multi-dimentional cancer genomics data

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]

AnaGalhoz37/wppi

Weighting protein-protein interactions

villabioinfo/txGeneNetwork

Workflow for constructing Pathway-Gene-Transcript expression networks

luciorq/txGeneNetwork

Workflow for constructing Pathway-Gene-Transcript expression networks

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