An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "GraphAndNetwork" keyword

Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 4 months ago - 61 dependent packages - 1.93 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 4 months ago - 49 dependent packages - 1.39 million downloads total - 1 maintainer
rWikiPathways 1.30.0
rWikiPathways - R client library for the WikiPathways API
6 versions - Latest release: 3 months ago - 5 dependent packages - 77.6 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 3 months ago - 101 dependent packages - 3.48 million downloads total - 1 maintainer
CIMICE 1.18.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
6 versions - Latest release: 3 months ago - 8.64 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 4 months ago - 33 dependent packages - 1.92 million downloads total - 1 maintainer
CausalR 1.42.0
Causal network analysis methods
6 versions - Latest release: 4 months ago - 20.4 thousand downloads total - 2 maintainers
Top 6.5% on bioconductor.org
goProfiles 1.72.0
goProfiles: an R package for the statistical analysis of functional profiles
6 versions - Latest release: 4 months ago - 1 dependent package - 53.4 thousand downloads total - 1 maintainer
Rigraphlib 1.2.0
igraph library as an R package
2 versions - Latest release: 3 months ago - 15.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.6.2
Interactive visualization and manipulation of nested networks
8 versions - Latest release: 8 days ago - 4 dependent packages - 63.7 thousand downloads total - 1 maintainer
hipathia 3.9.0
HiPathia: High-throughput Pathway Analysis
6 versions - Latest release: 4 months ago - 19.9 thousand downloads total - 1 maintainer
plotGrouper 1.28.0
Shiny app GUI wrapper for ggplot with built-in statistical analysis
6 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
keggorthology 2.62.0
graph support for KO, KEGG Orthology
6 versions - Latest release: 4 months ago - 1 dependent package - 53.3 thousand downloads total - 1 maintainer
dcanr 1.26.0
Differential co-expression/association network analysis
6 versions - Latest release: 3 months ago - 1 dependent package - 17.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 4.9% on bioconductor.org
rsbml 2.68.0
R support for SBML, using libsbml
6 versions - Latest release: 4 months ago - 3 dependent packages - 64 thousand downloads total - 1 maintainer
sparsenetgls 1.28.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
6 versions - Latest release: 4 months ago - 11.3 thousand downloads total - 1 maintainer
spqn 1.22.0
Spatial quantile normalization
6 versions - Latest release: 3 months ago - 10.5 thousand downloads total - 5 stars on GitHub - 1 maintainer
glmSparseNet 1.28.0
Network Centrality Metrics for Elastic-Net Regularized Models
7 versions - Latest release: 3 months ago - 107 thousand downloads total - 3 stars on GitHub - 1 maintainer
SBGNview 1.24.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
6 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 28 stars on GitHub - 1 maintainer
PhenoGeneRanker 1.18.0
PhenoGeneRanker: A gene and phenotype prioritization tool
6 versions - Latest release: 4 months ago - 7.51 thousand downloads total - 1 maintainer
Pedixplorer 1.6.0
Pedigree Functions
4 versions - Latest release: 3 months ago - 5.35 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
BioNet 1.70.0
Routines for the functional analysis of biological networks
6 versions - Latest release: 3 months ago - 3 dependent packages - 85.3 thousand downloads total - 1 maintainer
enrichTF 1.20.0 removed
Transcription Factors Enrichment Analysis
3 versions - Latest release: almost 2 years ago - 7.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
netOmics 1.12.0 removed
Multi-Omics (time-course) network-based integration and interpretation
4 versions - Latest release: over 1 year ago - 2.76 thousand downloads total - 14 stars on GitHub - 1 maintainer
KBoost 1.18.0
Inference of gene regulatory networks from gene expression data
6 versions - Latest release: 3 months ago - 7.78 thousand downloads total - 4 stars on GitHub - 1 maintainer
wppi 1.18.0
Weighting protein-protein interactions
7 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
transcriptogramer 1.32.0
Transcriptional analysis based on transcriptograms
6 versions - Latest release: 3 months ago - 15.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
PathoStat 1.36.0
PathoStat Statistical Microbiome Analysis Package
6 versions - Latest release: 3 months ago - 19.4 thousand downloads total - 8 stars on GitHub - 2 maintainers
syntenet 1.12.0
Inference And Analysis Of Synteny Networks
10 versions - Latest release: 3 months ago - 1 dependent package - 11 thousand downloads total - 36 stars on GitHub - 1 maintainer
epiregulon.extra 1.6.0
Companion package to epiregulon with additional plotting, differential and graph functions
7 versions - Latest release: 3 months ago - 5.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
netZooR 1.14.0
A menagerie of methods for the inference and analysis of gene regulatory networks
6 versions - Latest release: 3 months ago - 6.21 thousand downloads total - 113 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
SPIA 2.62.0
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation a...
6 versions - Latest release: 3 months ago - 3 dependent packages - 141 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.56.0
GRAPH Interaction from pathway Topological Environment
6 versions - Latest release: 4 months ago - 11 dependent packages - 395 thousand downloads total - 8 stars on GitHub - 1 maintainer
gsean 1.30.0
Gene Set Enrichment Analysis with Networks
6 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAlignment 1.74.0
GraphAlignment
6 versions - Latest release: 3 months ago - 35.9 thousand downloads total - 1 maintainer
MOGAMUN 1.20.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
6 versions - Latest release: 3 months ago - 9.82 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
qpgraph 2.44.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
6 versions - Latest release: 3 months ago - 1 dependent package - 70.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
SBMLR 2.6.0
SBML-R Interface and Analysis Tools
6 versions - Latest release: 3 months ago - 37.7 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.58.0
Pathways from the NCI Pathways Database
6 versions - Latest release: 4 months ago - 1 dependent package - 33.6 thousand downloads total - 1 maintainer
BatchQC 2.6.1
Batch Effects Quality Control Software
7 versions - Latest release: 11 days ago - 29.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
netSmooth 1.30.0
Network smoothing for scRNAseq
6 versions - Latest release: 3 months ago - 1 dependent package - 15.9 thousand downloads total - 28 stars on GitHub - 1 maintainer
MAGAR 1.18.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
6 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
PanViz 1.10.0 removed
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
5 versions - Latest release: 10 months ago - 3.39 thousand downloads total - 3 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance
6 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
VennDetail 1.26.0
Comprehensive Visualization and Analysis of Multi-Set Intersections
6 versions - Latest release: 3 months ago - 22 thousand downloads total - 24 stars on GitHub - 1 maintainer
BioNERO 1.18.0
Biological Network Reconstruction Omnibus
9 versions - Latest release: 3 months ago - 1 dependent package - 24.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
paircompviz 1.48.0
Multiple comparison test visualization
6 versions - Latest release: 3 months ago - 24.1 thousand downloads total - 1 maintainer
poem 1.2.0
POpulation-based Evaluation Metrics
3 versions - Latest release: 3 months ago - 2.58 thousand downloads total - 8 stars on GitHub - 1 maintainer
fgga 1.18.0
Hierarchical ensemble method based on factor graph
7 versions - Latest release: 3 months ago - 8.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
SGCP 1.10.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
9 versions - Latest release: 26 days ago - 7.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0 removed
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
5 versions - Latest release: 10 months ago - 27.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
FELLA 1.30.0
Interpretation and enrichment for metabolomics data
6 versions - Latest release: 3 months ago - 23.2 thousand downloads total - 1 maintainer
NetPathMiner 1.46.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
6 versions - Latest release: 3 months ago - 26.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
hypergraph 1.82.0
A package providing hypergraph data structures
6 versions - Latest release: 4 months ago - 3 dependent packages - 62 thousand downloads total - 1 maintainer
QuaternaryProd 1.44.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
6 versions - Latest release: 3 months ago - 18.6 thousand downloads total - 1 maintainer
ternarynet 1.54.0
Ternary Network Estimation
6 versions - Latest release: 3 months ago - 25.7 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.40.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
7 versions - Latest release: 3 months ago - 5 dependent packages - 74.8 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
DEGraph 1.62.0
Two-sample tests on a graph
6 versions - Latest release: 3 months ago - 1 dependent package - 33.4 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.70.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
6 versions - Latest release: 3 months ago - 13 dependent packages - 763 thousand downloads total - 1 maintainer
PANR 1.56.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...
6 versions - Latest release: 3 months ago - 29 thousand downloads total - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series
6 versions - Latest release: 3 months ago - 30 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.50.0
a tool set for pathway based data integration and visualization
6 versions - Latest release: 3 months ago - 9 dependent packages - 690 thousand downloads total - 41 stars on GitHub - 1 maintainer
rTRMui 1.48.0
A shiny user interface for rTRM
6 versions - Latest release: 3 months ago - 23.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
mirIntegrator 1.40.0
Integrating microRNA expression into signaling pathways for pathway analysis
6 versions - Latest release: 3 months ago - 19 thousand downloads total - 1 stars on GitHub - 1 maintainer
ANF 1.32.0
Affinity Network Fusion for Complex Patient Clustering
7 versions - Latest release: 3 months ago - 17.3 thousand downloads total - 1 maintainer
netresponse 1.70.0
Functional Network Analysis
6 versions - Latest release: 3 months ago - 32.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
nethet 1.42.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
6 versions - Latest release: 3 months ago - 20.3 thousand downloads total - 2 maintainers
splineTimeR 1.38.0
Time-course differential gene expression data analysis using spline regression models followed by...
6 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 2 maintainers
RGraph2js 1.38.0
Convert a Graph into a D3js Script
6 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 1 maintainer
Top 6.9% on bioconductor.org
biocGraph 1.72.0
Graph examples and use cases in Bioinformatics
6 versions - Latest release: 3 months ago - 1 dependent package - 63.4 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
hyperdraw 1.62.0
Visualizing Hypergaphs
6 versions - Latest release: 3 months ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.68.0
Mutual Information NETworks
6 versions - Latest release: 3 months ago - 9 dependent packages - 166 thousand downloads total - 1 maintainer
DART 1.58.0
Denoising Algorithm based on Relevance network Topology
6 versions - Latest release: 3 months ago - 32.1 thousand downloads total - 1 maintainer
PPInfer 1.36.0
Inferring functionally related proteins using protein interaction networks
6 versions - Latest release: 3 months ago - 1 dependent package - 20.3 thousand downloads total - 1 maintainer
EGAD 1.38.0
Extending guilt by association by degree
6 versions - Latest release: 3 months ago - 21.7 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
RTN 2.34.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
6 versions - Latest release: 3 months ago - 3 dependent packages - 40.3 thousand downloads total - 1 maintainer
ClusterFoldSimilarity 1.6.0
Calculate similarity of clusters from different single cell samples using foldchanges
4 versions - Latest release: 3 months ago - 4.96 thousand downloads total - 1 maintainer
OmnipathR 3.18.4
OmniPath web service client and more
11 versions - Latest release: 26 days ago - 3 dependent packages - 63.1 thousand downloads total - 1 maintainer
tidysbml 1.4.0
Extract SBML's data into dataframes
3 versions - Latest release: 3 months ago - 3.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
RITAN 1.34.0
Rapid Integration of Term Annotation and Network resources
6 versions - Latest release: 3 months ago - 15.5 thousand downloads total - 1 maintainer
rScudo 1.26.0
Signature-based Clustering for Diagnostic Purposes
7 versions - Latest release: 4 months ago - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy
7 versions - Latest release: 3 months ago - 25.6 thousand downloads total - 1 maintainer
fobitools 1.18.0
Tools for Manipulating the FOBI Ontology
6 versions - Latest release: 3 months ago - 8.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
R3CPET 1.42.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
7 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
pairkat 1.16.0
PaIRKAT
6 versions - Latest release: 4 months ago - 8.03 thousand downloads total - 0 stars on GitHub - 1 maintainer
RTNduals 1.34.0
Analysis of co-regulation and inference of 'dual regulons'
6 versions - Latest release: 3 months ago - 1 dependent package - 16.9 thousand downloads total - 2 maintainers
GSEABenchmarkeR 1.30.0
Reproducible GSEA Benchmarking
7 versions - Latest release: 3 months ago - 2 dependent packages - 17.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
martini 1.30.0
GWAS Incorporating Networks
6 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
ibh 1.58.0
Interaction Based Homogeneity for Evaluating Gene Lists
6 versions - Latest release: 3 months ago - 28.9 thousand downloads total - 1 maintainer
RCyjs 2.32.0
Display and manipulate graphs in cytoscape.js
6 versions - Latest release: 3 months ago - 21.3 thousand downloads total - 1 maintainer
GRaNIE 1.14.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...
6 versions - Latest release: 3 months ago - 9.81 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
GENIE3 1.32.0
GEne Network Inference with Ensemble of trees
6 versions - Latest release: 3 months ago - 2 dependent packages - 129 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MVCClass 1.84.0
Model-View-Controller (MVC) Classes
6 versions - Latest release: 3 months ago - 1 dependent package - 40.2 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAT 1.82.0
Graph Theoretic Association Tests
6 versions - Latest release: 3 months ago - 38.2 thousand downloads total - 1 maintainer
RTNsurvival 1.34.0
Survival analysis using transcriptional networks inferred by the RTN package
6 versions - Latest release: 3 months ago - 15.6 thousand downloads total - 2 maintainers
Pigengene 1.35.0
Infers biological signatures from gene expression data
6 versions - Latest release: 3 months ago - 1 dependent package - 20.8 thousand downloads total - 1 maintainer
rTRM 1.48.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
6 versions - Latest release: 3 months ago - 1 dependent package - 29 thousand downloads total - 3 stars on GitHub - 1 maintainer
ReactomeGraph4R 1.18.0
Interface for the Reactome Graph Database
7 versions - Latest release: 3 months ago - 4.49 thousand downloads total - 6 stars on GitHub - 1 maintainer
GWENA 1.20.0
Pipeline for augmented co-expression analysis
6 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 18 stars on GitHub - 1 maintainer
TreeAndLeaf 1.22.0
Displaying binary trees with focus on dendrogram leaves
6 versions - Latest release: 3 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
Related Keywords
Software 151 Network 91 GeneExpression 53 Pathways 48 Visualization 38 NetworkInference 37 SystemsBiology 32 Microarray 29 Clustering 29 GeneSetEnrichment 28 NetworkEnrichment 28 RNASeq 26 DifferentialExpression 25 KEGG 23 ImmunoOncology 21 GeneRegulation 17 Transcription 16 Transcriptomics 16 Sequencing 15 Metabolomics 14 Regression 13 StatisticalMethod 13 Classification 12 SingleCell 11 BiomedicalInformatics 11 Reactome 11 Genetics 10 GO 10 DimensionReduction 9 Proteomics 9 GeneTarget 9 ThirdPartyClient 9 Normalization 8 Bayesian 8 DataImport 8 Annotation 8 bioinformatics 7 QualityControl 6 r 6 mRNAMicroarray 6 DataRepresentation 6 GenePrediction 6 CellBiology 6 Preprocessing 5 Survival 5 FunctionalGenomics 5 MultipleComparison 5 PrincipalComponent 5 GeneSignaling 5 GUI 4 r-package 4 SNP 4 GeneticVariability 4 ATACSeq 4 GenomeWideAssociation 4 Infrastructure 4 TwoChannel 3 TimeCourse 3 NeuralNetwork 3 MassSpectrometry 3 DecisionTree 3 bioconductor 3 FeatureExtraction 3 gene-regulatory-network 2 DNASeq 2 systems-biology 2 network-analysis 2 HiC 2 BatchEffect 2 enrichment-analysis 2 SomaticMutation 2 genomics 2 DNAMethylation 2 Epigenetics 2 CellBasedAssays 2 ReportWriting 2 networks 2 ChIPSeq 2 Spatial 2 rstats 2 Phylogenetics 2 network-science 2 pathways 2 CopyNumberVariation 2 LinkageDisequilibrium 1 cerna 1 TissueMicroarray 1 data-access 1 transcriptomics 1 pipeline 1 gene 1 co-expression 1 rpackage 1 snps 1 BiologicalQuestion 1 gwas 1 u24ca289073 1 bioconductor-package 1 transcription-facto 1 dirichlet-process-mixtures 1