bioconductor.org "Network" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Network" keyword.
Informeasure 1.18.0
R implementation of information measures6 versions - Latest release: 3 months ago - 6.94 thousand downloads total - 3 stars on GitHub - 1 maintainer
CARNIVAL 2.18.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...5 versions - Latest release: 3 months ago - 2 dependent packages - 15.4 thousand downloads total - 59 stars on GitHub - 1 maintainer
mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
DeProViR 1.4.0
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...4 versions - Latest release: 2 months ago - 1.78 thousand downloads total - 1 stars on GitHub - 1 maintainer
BulkSignalR 1.0.2
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...2 versions - Latest release: about 1 month ago - 1.67 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioCor 1.32.0
Functional similarities5 versions - Latest release: 2 months ago - 18.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
MOGAMUN 1.18.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks5 versions - Latest release: 2 months ago - 7.53 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 33 dependent packages - 1.68 million downloads total - 1 maintainer
RBGL 1.84.0
An interface to the BOOST graph library5 versions - Latest release: 3 months ago - 33 dependent packages - 1.68 million downloads total - 1 maintainer
rrvgo 1.20.0
Reduce + Visualize GO7 versions - Latest release: 3 months ago - 30.3 thousand downloads total - 30 stars on GitHub - 1 maintainer
netZooR 1.11.0
Unified methods for the inference and analysis of gene regulatory networks5 versions - Latest release: 3 months ago - 5.48 thousand downloads total - 109 stars on GitHub - 1 maintainer
dominoSignal 1.2.0
Cell Communication Analysis for Single Cell RNA Sequencing2 versions - Latest release: 2 months ago - 2.01 thousand downloads total - 5 stars on GitHub - 1 maintainer
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization5 versions - Latest release: 3 months ago - 23.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
GRENITS 1.60.0
Gene Regulatory Network Inference Using Time Series5 versions - Latest release: 3 months ago - 27.6 thousand downloads total - 1 maintainer
MSstatsBioNet 1.0.0
Network Analysis for MS-based Proteomics Experiments1 version - Latest release: 3 months ago - 1.14 thousand downloads total - 2 stars on GitHub - 1 maintainer
fedup 1.16.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways5 versions - Latest release: 3 months ago - 6.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
QUBIC 1.36.0
An R package for qualitative biclustering in support of gene co-expression analyses5 versions - Latest release: 3 months ago - 2 dependent packages - 30.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
6 versions - Latest release: 4 days ago - 15 dependent packages - 96.3 thousand downloads total - 52 stars on GitHub - 1 maintainer
RCy3 2.28.1
Functions to Access and Control Cytoscape6 versions - Latest release: 4 days ago - 15 dependent packages - 96.3 thousand downloads total - 52 stars on GitHub - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models5 versions - Latest release: 3 months ago - 4 dependent packages - 13.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
5 versions - Latest release: 2 months ago - 5 dependent packages - 62.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
EnrichmentBrowser 2.38.0
Seamless navigation through combined results of set-based and network-based enrichment analysis5 versions - Latest release: 2 months ago - 5 dependent packages - 62.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
SingleCellSignalR 1.20.0
Cell Signalling Using Single Cell RNAseq Data Analysis5 versions - Latest release: 3 months ago - 3 dependent packages - 18.8 thousand downloads total - 1 maintainer
BioNERO 1.16.0
Biological Network Reconstruction Omnibus7 versions - Latest release: 3 months ago - 1 dependent package - 19.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
BiGGR 1.44.0
Constraint based modeling in R using metabolic reconstruction databases5 versions - Latest release: 2 months ago - 31.6 thousand downloads total - 2 maintainers
Top 2.7% on bioconductor.org
7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
TCGAbiolinks 2.36.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
miRLAB 1.38.0
Dry lab for exploring miRNA-mRNA relationships5 versions - Latest release: 2 months ago - 18.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
FELLA 1.28.0
Interpretation and enrichment for metabolomics data5 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
doubletrouble 1.8.0
Identification and classification of duplicated genes11 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 27 stars on GitHub - 1 maintainer
DEsubs 1.34.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 2 maintainers
gatom 1.6.0
Finding an Active Metabolic Module in Atom Transition Network4 versions - Latest release: 3 months ago - 4.57 thousand downloads total - 7 stars on GitHub - 1 maintainer
cogeqc 1.12.0
Systematic quality checks on comparative genomics analyses6 versions - Latest release: 3 months ago - 6.54 thousand downloads total - 8 stars on GitHub - 1 maintainer
miaSim 1.14.0
Microbiome Data Simulation5 versions - Latest release: 3 months ago - 7.38 thousand downloads total - 22 stars on GitHub - 1 maintainer
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...5 versions - Latest release: 2 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
regutools 1.20.0
regutools: an R package for data extraction from RegulonDB5 versions - Latest release: 2 months ago - 8.67 thousand downloads total - 5 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.28.1
Reproducible GSEA Benchmarking6 versions - Latest release: about 2 months ago - 2 dependent packages - 14.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
syntenet 1.10.0
Inference And Analysis Of Synteny Networks8 versions - Latest release: 3 months ago - 1 dependent package - 7.84 thousand downloads total - 30 stars on GitHub - 1 maintainer
netboost 2.16.0
Network Analysis Supported by Boosting5 versions - Latest release: 3 months ago - 8.54 thousand downloads total - 1 maintainer
DeepPINCS 1.16.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning5 versions - Latest release: 3 months ago - 2 dependent packages - 7.41 thousand downloads total - 1 maintainer
CCPlotR 1.6.0
Plots For Visualising Cell-Cell Interactions4 versions - Latest release: 3 months ago - 4.5 thousand downloads total - 44 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
interactiveDisplay 1.46.0
Package for enabling powerful shiny web displays of Bioconductor objects5 versions - Latest release: 3 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
GWENA 1.18.0
Pipeline for augmented co-expression analysis5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 881 thousand downloads total - 1 maintainer
interactiveDisplayBase 1.46.0
Base package for enabling powerful shiny web displays of Bioconductor objects5 versions - Latest release: 3 months ago - 3 dependent packages - 881 thousand downloads total - 1 maintainer
DriverNet 1.48.0
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer5 versions - Latest release: 3 months ago - 25.7 thousand downloads total - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more7 versions - Latest release: 3 months ago - 3 dependent packages - 44 thousand downloads total - 1 maintainer
pageRank 1.18.0
Temporal and Multiplex PageRank for Gene Regulatory Network Analysis5 versions - Latest release: 3 months ago - 7.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
PathNet 1.48.0
An R package for pathway analysis using topological information5 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 1 maintainer
lionessR 1.22.0
Modeling networks for individual samples using LIONESS5 versions - Latest release: 3 months ago - 9.5 thousand downloads total - 22 stars on GitHub - 1 maintainer
GNET2 1.24.0
Constructing gene regulatory networks from expression data through functional module inference5 versions - Latest release: 3 months ago - 9.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
rScudo 1.24.0
Signature-based Clustering for Diagnostic Purposes6 versions - Latest release: 3 months ago - 9.68 thousand downloads total - 4 stars on GitHub - 1 maintainer
diffuStats 1.28.0
Diffusion scores on biological networks5 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
GDCRNATools 1.28.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
RCX 1.12.0
R package implementing the Cytoscape Exchange (CX) format5 versions - Latest release: 3 months ago - 1 dependent package - 7.22 thousand downloads total - 8 stars on GitHub - 1 maintainer
pareg 1.12.0
Pathway enrichment using a regularized regression approach5 versions - Latest release: 3 months ago - 4.14 thousand downloads total - 7 stars on GitHub - 1 maintainer
omicsViewer 1.12.0
Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omics...5 versions - Latest release: 3 months ago - 6.31 thousand downloads total - 4 stars on GitHub - 1 maintainer
MOMA 1.20.0
Multi Omic Master Regulator Analysis5 versions - Latest release: 3 months ago - 8.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
IMMAN 1.28.0
Interlog protein network reconstruction by Mapping and Mining ANalysis5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 maintainer
decoupleR 2.14.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data6 versions - Latest release: 2 months ago - 3 dependent packages - 54.6 thousand downloads total - 256 stars on GitHub - 1 maintainer
oppti 1.21.0
Outlier Protein and Phosphosite Target Identifier5 versions - Latest release: 3 months ago - 7.72 thousand downloads total - 2 stars on GitHub - 1 maintainer
ReactomeGraph4R 1.16.0
Interface for the Reactome Graph Database6 versions - Latest release: 3 months ago - 4.21 thousand downloads total - 6 stars on GitHub - 1 maintainer
ANF 1.30.0
Affinity Network Fusion for Complex Patient Clustering6 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 1 maintainer
MIRit 1.4.1
Integrate microRNA and gene expression to decipher pathway complexity5 versions - Latest release: about 2 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
ndexr 1.30.0
NDEx R client library5 versions - Latest release: 2 months ago - 14 thousand downloads total - 9 stars on GitHub - 1 maintainer
cosmosR 1.16.0
COSMOS (Causal Oriented Search of Multi-Omic Space)5 versions - Latest release: 3 months ago - 8.53 thousand downloads total - 61 stars on GitHub - 1 maintainer
gsean 1.28.0
Gene Set Enrichment Analysis with Networks5 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
bnem 1.16.0
Training of logical models from indirect measurements of perturbation experiments5 versions - Latest release: 3 months ago - 7.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
LiquidAssociation 1.62.0
LiquidAssociation5 versions - Latest release: 3 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
cageminer 1.14.0
Candidate Gene Miner5 versions - Latest release: 3 months ago - 6.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
SPEM 1.48.0
S-system parameter estimation method5 versions - Latest release: 3 months ago - 1 dependent package - 24.3 thousand downloads total - 1 maintainer
MetID 1.26.0
Network-based prioritization of putative metabolite IDs5 versions - Latest release: 3 months ago - 9.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
PhenoGeneRanker 1.16.0
PhenoGeneRanker: A gene and phenotype prioritization tool5 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 59.8 thousand downloads total - 1 maintainer
rsbml 2.66.0
R support for SBML, using libsbml5 versions - Latest release: 3 months ago - 3 dependent packages - 59.8 thousand downloads total - 1 maintainer
tidysbml 1.2.0
Extract SBML's data into dataframes2 versions - Latest release: 3 months ago - 1.76 thousand downloads total - 1 stars on GitHub - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks5 versions - Latest release: 3 months ago - 1 dependent package - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
RGMQL 1.28.0
GenoMetric Query Language for R/Bioconductor6 versions - Latest release: 3 months ago - 8.29 thousand downloads total - 1 maintainer
Path2PPI 1.38.0
Prediction of pathway-related protein-protein interaction networks5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 1 maintainer
ternarynet 1.52.0
Ternary Network Estimation5 versions - Latest release: 3 months ago - 23.2 thousand downloads total - 1 maintainer
epiregulon 1.4.0
Gene regulatory network inference from single cell epigenomic data4 versions - Latest release: 3 months ago - 1 dependent package - 3.07 thousand downloads total - 12 stars on GitHub - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 3 months ago - 6.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
XINA 1.26.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis5 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
RITAN 1.32.0
Rapid Integration of Term Annotation and Network resources5 versions - Latest release: 3 months ago - 13.4 thousand downloads total - 1 maintainer
MODA 1.34.0
MODA: MOdule Differential Analysis for weighted gene co-expression network5 versions - Latest release: 3 months ago - 15.3 thousand downloads total - 1 maintainer
CNORfuzzy 1.50.0
Addon to CellNOptR: Fuzzy Logic5 versions - Latest release: 3 months ago - 25.7 thousand downloads total - 1 maintainer
Pigengene 1.34.0
Infers biological signatures from gene expression data5 versions - Latest release: 3 months ago - 1 dependent package - 18.5 thousand downloads total - 1 maintainer
rTRMui 1.46.0
A shiny user interface for rTRM5 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
ADImpute 1.18.0
Adaptive Dropout Imputer (ADImpute)5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
netresponse 1.68.0
Functional Network Analysis5 versions - Latest release: 3 months ago - 30 thousand downloads total - 3 stars on GitHub - 1 maintainer
PCAN 1.36.0
Phenotype Consensus ANalysis (PCAN)5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
TreeAndLeaf 1.20.0
Displaying binary trees with focus on dendrogram leaves5 versions - Latest release: 3 months ago - 1 dependent package - 11.8 thousand downloads total - 1 maintainer
SANTA 2.44.0
Spatial Analysis of Network Associations5 versions - Latest release: 3 months ago - 22.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
netprioR 1.34.0
A model for network-based prioritisation of genes5 versions - Latest release: 3 months ago - 12.5 thousand downloads total - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data5 versions - Latest release: 3 months ago - 5.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
RegEnrich 1.18.1
Gene regulator enrichment analysis7 versions - Latest release: about 2 months ago - 8.64 thousand downloads total - 1 maintainer
epiregulon.extra 1.4.0
Companion package to epiregulon with additional plotting, differential and graph functions6 versions - Latest release: 3 months ago - 3.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
netDx 1.20.0
Network-based patient classifier5 versions - Latest release: 3 months ago - 6.11 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 9 dependent packages - 138 thousand downloads total - 1 maintainer
minet 3.66.0
Mutual Information NETworks5 versions - Latest release: 3 months ago - 9 dependent packages - 138 thousand downloads total - 1 maintainer
CTDquerier 2.16.0
Package for CTDbase data query, visualization and downstream analysis5 versions - Latest release: 3 months ago - 9.52 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 34.9 thousand downloads total - 1 maintainer
RTN 2.32.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons5 versions - Latest release: 3 months ago - 3 dependent packages - 34.9 thousand downloads total - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions5 versions - Latest release: 3 months ago - 7.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 30.8 thousand downloads total - 1 maintainer
DEGraph 1.60.0
Two-sample tests on a graph5 versions - Latest release: 3 months ago - 1 dependent package - 30.8 thousand downloads total - 1 maintainer
AMARETTO 1.24.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...5 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
HPiP 1.14.0
Host-Pathogen Interaction Prediction5 versions - Latest release: 3 months ago - 6.05 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software
185
GraphAndNetwork
90
GeneExpression
79
Pathways
60
NetworkInference
51
SystemsBiology
45
NetworkEnrichment
43
DifferentialExpression
39
Clustering
29
GeneSetEnrichment
27
GeneRegulation
27
RNASeq
27
Visualization
26
Microarray
24
Transcriptomics
22
KEGG
22
ImmunoOncology
22
Transcription
20
Sequencing
18
Classification
17
StatisticalMethod
17
Proteomics
16
SingleCell
15
Metabolomics
14
GeneTarget
14
Regression
13
bioinformatics
12
GO
12
Reactome
11
DataImport
11
BiomedicalInformatics
11
Bayesian
10
Genetics
10
FunctionalGenomics
10
DataRepresentation
9
Normalization
9
QualityControl
8
CellBiology
8
DimensionReduction
8
r
8
DNAMethylation
8
DifferentialMethylation
8
mRNAMicroarray
7
Annotation
7
Preprocessing
7
Survival
7
GenePrediction
7
GeneSignaling
6
GUI
6
ThirdPartyClient
6
MethylationArray
6
bioconductor
6
TimeCourse
6
MultipleComparison
5
GenomeWideAssociation
5
Infrastructure
5
rstats
5
NeuralNetwork
5
miRNA
4
r-package
4
FunctionalPrediction
4
pathways
4
Coverage
4
DNASeq
4
ATACSeq
4
SNP
4
TwoChannel
4
BatchEffect
3
CopyNumberVariation
3
genomics
3
FeatureExtraction
3
Epigenetics
3
comparative-genomics
3
Phylogenetics
3
GeneticVariability
3
ComparativeGenomics
3
network
3
bioconductor-package
3
networks
3
CellBasedAssays
3
MassSpectrometry
3
PrincipalComponent
3
DecisionTree
3
tcga
2
OneChannel
2
systems-biology
2
AnnotationData
2
AlternativeSplicing
2
Spatial
2
ShinyApps
2
network-analysis
2
transcriptomics
2
pathway-enrichment-analysis
2
WorkflowStep
2
ChIPSeq
2
BiologicalQuestion
2
SomaticMutation
2
SequenceMatching
2
VariantAnnotation
2
visualization
2