bioconductor.org "Network" keyword
goatea 1.0.2
Interactive Exploration of GSEA by the GOAT Method2 versions - Latest release: 16 days ago - 228 downloads total - 2 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
6 versions - Latest release: 4 months ago - 33 dependent packages - 1.92 million downloads total - 1 maintainer
RBGL 1.86.0
An interface to the BOOST graph library6 versions - Latest release: 4 months ago - 33 dependent packages - 1.92 million downloads total - 1 maintainer
iModMix 1.0.0
Integrative Modules for Multi-Omics Data1 version - Latest release: 4 months ago - 936 downloads total - 2 stars on GitHub - 1 maintainer
PPInfer 1.36.0
Inferring functionally related proteins using protein interaction networks6 versions - Latest release: 3 months ago - 1 dependent package - 20.8 thousand downloads total - 1 maintainer
MetaboSignal 1.40.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways7 versions - Latest release: 3 months ago - 22.3 thousand downloads total - 2 maintainers
Top 2.1% on bioconductor.org
8 versions - Latest release: 3 months ago - 14 dependent packages - 2.04 million downloads total - 1 maintainer
GOSemSim 2.36.0
GO-terms Semantic Similarity Measures8 versions - Latest release: 3 months ago - 14 dependent packages - 2.04 million downloads total - 1 maintainer
RITAN 1.34.0
Rapid Integration of Term Annotation and Network resources6 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 1 maintainer
SPEM 1.50.0
S-system parameter estimation method6 versions - Latest release: 4 months ago - 1 dependent package - 26.9 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
6 versions - Latest release: 3 months ago - 9 dependent packages - 167 thousand downloads total - 1 maintainer
minet 3.68.0
Mutual Information NETworks6 versions - Latest release: 3 months ago - 9 dependent packages - 167 thousand downloads total - 1 maintainer
PIUMA 1.6.1
Phenotypes Identification Using Mapper from topological data Analysis5 versions - Latest release: 3 days ago - 4.83 thousand downloads total - 5 stars on GitHub - 1 maintainer
COSNet 1.44.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings6 versions - Latest release: 3 months ago - 21.6 thousand downloads total - 1 stars on GitHub
RLassoCox 1.18.0
A reweighted Lasso-Cox by integrating gene interaction information6 versions - Latest release: 3 months ago - 8.56 thousand downloads total - 3 stars on GitHub - 1 maintainer
netresponse 1.70.0
Functional Network Analysis6 versions - Latest release: 3 months ago - 33.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
tidysbml 1.4.0
Extract SBML's data into dataframes3 versions - Latest release: 4 months ago - 3.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
RGraph2js 1.38.0
Convert a Graph into a D3js Script6 versions - Latest release: 3 months ago - 17.4 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
6 versions - Latest release: 4 months ago - 47.5 thousand downloads total - 2 maintainers
GDCRNATools 1.30.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...6 versions - Latest release: 4 months ago - 47.5 thousand downloads total - 2 maintainers
mirIntegrator 1.40.0
Integrating microRNA expression into signaling pathways for pathway analysis6 versions - Latest release: 4 months ago - 19.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
rTRM 1.48.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks6 versions - Latest release: 4 months ago - 1 dependent package - 29.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy7 versions - Latest release: 3 months ago - 26.1 thousand downloads total - 1 maintainer
CARNIVAL 2.20.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...6 versions - Latest release: 4 months ago - 2 dependent packages - 19.8 thousand downloads total - 60 stars on GitHub - 1 maintainer
rTRMui 1.48.0
A shiny user interface for rTRM6 versions - Latest release: 4 months ago - 24.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
MOMA 1.22.0
Multi Omic Master Regulator Analysis6 versions - Latest release: 3 months ago - 11 thousand downloads total - 5 stars on GitHub - 1 maintainer
cosmosR 1.18.1
COSMOS (Causal Oriented Search of Multi-Omic Space)7 versions - Latest release: 4 days ago - 12 thousand downloads total - 62 stars on GitHub - 1 maintainer
BulkSignalR 1.2.2
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...6 versions - Latest release: 4 days ago - 5.43 thousand downloads total - 1 stars on GitHub - 1 maintainer
cliqueMS 1.24.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data7 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
GNET2 1.26.0
Constructing gene regulatory networks from expression data through functional module inference6 versions - Latest release: 4 months ago - 11.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
CEMiTool 1.34.0
Co-expression Modules identification Tool8 versions - Latest release: 3 months ago - 40.5 thousand downloads total - 1 maintainer
pairkat 1.16.0
PaIRKAT6 versions - Latest release: 4 months ago - 8.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
csdR 1.16.0
Differential gene co-expression6 versions - Latest release: 4 months ago - 7.82 thousand downloads total - 6 stars on GitHub - 1 maintainer
Path2PPI 1.40.0
Prediction of pathway-related protein-protein interaction networks6 versions - Latest release: 3 months ago - 20.2 thousand downloads total - 1 maintainer
BayesKnockdown 1.36.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data6 versions - Latest release: 3 months ago - 18 thousand downloads total - 1 maintainer
BioNAR 1.12.2
Biological Network Analysis in R11 versions - Latest release: 3 months ago - 8.39 thousand downloads total - 1 maintainer
regutools 1.22.0
regutools: an R package for data extraction from RegulonDB6 versions - Latest release: 4 months ago - 11.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 35.4 thousand downloads total - 1 maintainer
FGNet 3.44.0
Functional Gene Networks derived from biological enrichment analyses6 versions - Latest release: 3 months ago - 1 dependent package - 35.4 thousand downloads total - 1 maintainer
BiRewire 3.41.0
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), u...6 versions - Latest release: 3 months ago - 37.4 thousand downloads total - 1 maintainer
rrvgo 1.22.0
Reduce + Visualize GO8 versions - Latest release: 4 months ago - 43.9 thousand downloads total - 34 stars on GitHub - 1 maintainer
MODA 1.36.0
MODA: MOdule Differential Analysis for weighted gene co-expression network6 versions - Latest release: 3 months ago - 18.1 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
8 versions - Latest release: 3 months ago - 15 dependent packages - 120 thousand downloads total - 54 stars on GitHub - 1 maintainer
RCy3 2.30.1
Functions to Access and Control Cytoscape8 versions - Latest release: 3 months ago - 15 dependent packages - 120 thousand downloads total - 54 stars on GitHub - 1 maintainer
mosbi 1.16.0
Molecular Signature identification using Biclustering6 versions - Latest release: 3 months ago - 8.8 thousand downloads total - 1 maintainer
SingleCellSignalR 2.0.1
Cell Signalling Using Single-Cell RNA-seq or Proteomics Data6 versions - Latest release: 3 months ago - 3 dependent packages - 24.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
Pigengene 1.35.0
Infers biological signatures from gene expression data6 versions - Latest release: 3 months ago - 1 dependent package - 21.3 thousand downloads total - 1 maintainer
DEsubs 1.36.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...6 versions - Latest release: 4 months ago - 18.8 thousand downloads total - 2 maintainers
ceRNAnetsim 1.22.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)7 versions - Latest release: 4 months ago - 9.64 thousand downloads total - 5 stars on GitHub - 1 maintainer
RegEnrich 1.20.0
Gene regulator enrichment analysis8 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
6 versions - Latest release: 3 months ago - 2 dependent packages - 131 thousand downloads total - 1 maintainer
GENIE3 1.32.0
GEne Network Inference with Ensemble of trees6 versions - Latest release: 3 months ago - 2 dependent packages - 131 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
6 versions - Latest release: 3 months ago - 6 dependent packages - 49.9 thousand downloads total - 1 maintainer
CellNOptR 1.56.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...6 versions - Latest release: 3 months ago - 6 dependent packages - 49.9 thousand downloads total - 1 maintainer
epiNEM 1.34.0
epiNEM6 versions - Latest release: 4 months ago - 4 dependent packages - 19.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
levi 1.28.0
Landscape Expression Visualization Interface6 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 maintainer
AMOUNTAIN 1.36.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...6 versions - Latest release: 4 months ago - 1 dependent package - 22.6 thousand downloads total - 1 maintainer
MetID 1.28.0
Network-based prioritization of putative metabolite IDs6 versions - Latest release: 4 months ago - 12.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
diffuStats 1.30.0
Diffusion scores on biological networks6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
OmnipathR 3.18.4
OmniPath web service client and more11 versions - Latest release: about 1 month ago - 3 dependent packages - 65.8 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
7 versions - Latest release: 5 days ago - 3 dependent packages - 41 thousand downloads total - 1 maintainer
RTN 2.34.1
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons7 versions - Latest release: 5 days ago - 3 dependent packages - 41 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
interactiveDisplayBase 1.48.0
Base package for enabling powerful shiny web displays of Bioconductor objects6 versions - Latest release: 3 months ago - 3 dependent packages - 1.03 million downloads total - 1 maintainer
CBNplot 1.10.0
plot bayesian network inferred from gene expression data based on enrichment analysis results8 versions - Latest release: 4 months ago - 9.34 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
6 versions - Latest release: 3 months ago - 38.7 thousand downloads total - 1 maintainer
GraphAT 1.82.0
Graph Theoretic Association Tests6 versions - Latest release: 3 months ago - 38.7 thousand downloads total - 1 maintainer
R3CPET 1.42.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process7 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
rScudo 1.26.0
Signature-based Clustering for Diagnostic Purposes7 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
TreeAndLeaf 1.22.2
Displaying binary trees with focus on dendrogram leaves7 versions - Latest release: 5 days ago - 1 dependent package - 15 thousand downloads total - 1 maintainer
GmicR 1.24.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...6 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
pandaR 1.42.0
PANDA Algorithm6 versions - Latest release: 3 months ago - 1 dependent package - 25.3 thousand downloads total - 2 maintainers
ndexr 1.32.0
NDEx R client library6 versions - Latest release: 3 months ago - 16.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
DeepPINCS 1.18.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning6 versions - Latest release: 3 months ago - 2 dependent packages - 9.47 thousand downloads total - 1 maintainer
pageRank 1.20.0
Temporal and Multiplex PageRank for Gene Regulatory Network Analysis6 versions - Latest release: 4 months ago - 9.43 thousand downloads total - 0 stars on GitHub - 1 maintainer
iNETgrate 1.8.0
Integrates DNA methylation data with gene expression in a single gene network6 versions - Latest release: about 1 month ago - 5.72 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
8 versions - Latest release: 3 months ago - 13 dependent packages - 185 thousand downloads total - 1 maintainer
STRINGdb 2.22.0
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis8 versions - Latest release: 3 months ago - 13 dependent packages - 185 thousand downloads total - 1 maintainer
PCAN 1.38.0
Phenotype Consensus ANalysis (PCAN)6 versions - Latest release: 3 months ago - 18.3 thousand downloads total - 1 maintainer
CNORfuzzy 1.52.0
Addon to CellNOptR: Fuzzy Logic6 versions - Latest release: 3 months ago - 29.3 thousand downloads total - 1 maintainer
ReactomeGraph4R 1.18.0
Interface for the Reactome Graph Database7 versions - Latest release: 3 months ago - 4.58 thousand downloads total - 6 stars on GitHub - 1 maintainer
bioCancer 1.38.0
Interactive Multi-Omics Cancers Data Visualization and Analysis8 versions - Latest release: 4 months ago - 20 thousand downloads total - 21 stars on GitHub - 1 maintainer
scGraphVerse 1.0.0
scGraphVerse: A Gene Network Analysis Package1 version - Latest release: 4 months ago - 818 downloads total - 1 stars on GitHub - 1 maintainer
bnem 1.18.0
Training of logical models from indirect measurements of perturbation experiments6 versions - Latest release: 4 months ago - 9.29 thousand downloads total - 2 stars on GitHub - 1 maintainer
EGAD 1.38.0
Extending guilt by association by degree6 versions - Latest release: 3 months ago - 22.1 thousand downloads total - 1 maintainer
BiGGR 1.46.0
Constraint based modeling in R using metabolic reconstruction databases6 versions - Latest release: 3 months ago - 33.5 thousand downloads total - 2 maintainers
LiquidAssociation 1.64.0
LiquidAssociation6 versions - Latest release: 3 months ago - 1 dependent package - 34.8 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
7 versions - Latest release: 3 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
EGSEA 1.38.0
Ensemble of Gene Set Enrichment Analyses7 versions - Latest release: 3 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
KEGGlincs 1.36.0
Visualize all edges within a KEGG pathway and overlay LINCS data6 versions - Latest release: 3 months ago - 18.3 thousand downloads total - 2 maintainers
epiregulon 2.0.2
Gene regulatory network inference from single cell epigenomic data6 versions - Latest release: 3 months ago - 1 dependent package - 5.53 thousand downloads total - 12 stars on GitHub - 1 maintainer
GWENA 1.20.0
Pipeline for augmented co-expression analysis6 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 18 stars on GitHub - 1 maintainer
ANF 1.32.0
Affinity Network Fusion for Complex Patient Clustering7 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
7 versions - Latest release: 6 days ago - 51.3 thousand downloads total - 1 maintainer
ELMER 2.34.2
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes7 versions - Latest release: 6 days ago - 51.3 thousand downloads total - 1 maintainer
enrichViewNet 1.8.1
From functional enrichment results to biological networks7 versions - Latest release: about 1 month ago - 6.64 thousand downloads total - 5 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.30.0
Reproducible GSEA Benchmarking7 versions - Latest release: 4 months ago - 2 dependent packages - 18.4 thousand downloads total - 13 stars on GitHub - 1 maintainer
martini 1.30.0
GWAS Incorporating Networks6 versions - Latest release: 4 months ago - 14.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
SANTA 2.46.0
Spatial Analysis of Network Associations6 versions - Latest release: 3 months ago - 25.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
miaSim 1.16.0
Microbiome Data Simulation6 versions - Latest release: 3 months ago - 9.75 thousand downloads total - 22 stars on GitHub - 1 maintainer
netboost 2.18.1
Network Analysis Supported by Boosting7 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 maintainer
dominoSignal 1.4.0
Cell Communication Analysis for Single Cell RNA Sequencing3 versions - Latest release: 4 months ago - 3.74 thousand downloads total - 6 stars on GitHub - 1 maintainer
spatialHeatmap 2.16.3
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions16 versions - Latest release: about 1 month ago - 14.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
ADImpute 1.20.0
Adaptive Dropout Imputer (ADImpute)6 versions - Latest release: 3 months ago - 14.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
BioCor 1.34.0
Functional Similarities6 versions - Latest release: 4 months ago - 21.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
IMMAN 1.30.0
Interlog protein network reconstruction by Mapping and Mining ANalysis6 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
8 versions - Latest release: 4 months ago - 7 dependent packages - 573 thousand downloads total - 339 stars on GitHub - 2 maintainers
TCGAbiolinks 2.38.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data8 versions - Latest release: 4 months ago - 7 dependent packages - 573 thousand downloads total - 339 stars on GitHub - 2 maintainers
Moonlight2R 1.8.1
Identify oncogenes and tumor suppressor genes from omics data7 versions - Latest release: about 1 month ago - 6.5 thousand downloads total - 5 stars on GitHub - 1 maintainer
fedup 1.18.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways6 versions - Latest release: 4 months ago - 8.77 thousand downloads total - 7 stars on GitHub - 1 maintainer
rWikiPathways 1.30.0
rWikiPathways - R client library for the WikiPathways API6 versions - Latest release: 4 months ago - 5 dependent packages - 77.6 thousand downloads total - 17 stars on GitHub - 1 maintainer
CausalR 1.42.0
Causal network analysis methods6 versions - Latest release: 4 months ago - 20.4 thousand downloads total - 2 maintainers
decoupleR 2.16.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data7 versions - Latest release: 4 months ago - 3 dependent packages - 82.7 thousand downloads total - 281 stars on GitHub - 1 maintainer
CTDquerier 2.18.0
Package for CTDbase data query, visualization and downstream analysis6 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
Related Keywords
Software
189
GraphAndNetwork
91
GeneExpression
80
Pathways
61
NetworkInference
53
NetworkEnrichment
46
SystemsBiology
46
DifferentialExpression
41
Clustering
30
GeneSetEnrichment
29
Visualization
29
RNASeq
28
GeneRegulation
28
Transcriptomics
25
Microarray
24
KEGG
23
ImmunoOncology
22
Transcription
20
Proteomics
19
Sequencing
19
StatisticalMethod
17
SingleCell
16
Classification
16
Metabolomics
16
GeneTarget
14
Regression
13
bioinformatics
13
GO
12
Reactome
12
DataImport
12
Genetics
11
BiomedicalInformatics
11
FunctionalGenomics
11
Bayesian
10
DataRepresentation
9
Normalization
9
DNAMethylation
8
DifferentialMethylation
8
r
8
CellBiology
8
DimensionReduction
8
QualityControl
8
GUI
7
mRNAMicroarray
7
Survival
7
GenePrediction
7
Preprocessing
7
Annotation
7
TimeCourse
6
GeneSignaling
6
MethylationArray
6
ThirdPartyClient
6
bioconductor
6
MultipleComparison
5
GenomeWideAssociation
5
NeuralNetwork
5
rstats
5
r-package
4
SNP
4
ATACSeq
4
Coverage
4
DNASeq
4
pathways
4
Infrastructure
4
miRNA
4
TwoChannel
4
FunctionalPrediction
4
PrincipalComponent
4
GeneticVariability
3
Epigenetics
3
FeatureExtraction
3
network
3
genomics
3
CopyNumberVariation
3
CellBasedAssays
3
BatchEffect
3
MassSpectrometry
3
ShinyApps
3
bioconductor-package
3
ComparativeGenomics
3
Phylogenetics
3
network-analysis
3
comparative-genomics
3
DecisionTree
3
networks
3
AlternativeSplicing
2
evolutionary-genomics
2
CRISPR
2
pathway-analysis
2
PooledScreens
2
bioconductor-packages
2
OneChannel
2
Microbiome
2
SomaticMutation
2
pathway-enrichment-analysis
2
VariantAnnotation
2
systems-biology
2
ReportWriting
2
gene
2
BiologicalQuestion
2