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

bioconductor.org "GraphAndNetwork" keyword

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 - 3.51 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 5 months ago - 61 dependent packages - 1.94 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: 5 months ago - 49 dependent packages - 1.4 million downloads total - 1 maintainer
Pedixplorer 1.6.0
Pedigree Functions
4 versions - Latest release: 4 months ago - 5.81 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: 5 months ago - 33 dependent packages - 1.93 million downloads total - 1 maintainer
KBoost 1.18.0
Inference of gene regulatory networks from gene expression data
6 versions - Latest release: 4 months ago - 8.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
PathoStat 1.36.0
PathoStat Statistical Microbiome Analysis Package
6 versions - Latest release: 4 months ago - 19.8 thousand downloads total - 8 stars on GitHub - 2 maintainers
wppi 1.18.0
Weighting protein-protein interactions
7 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 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: 4 months ago - 38.3 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAlignment 1.74.0
GraphAlignment
6 versions - Latest release: 4 months ago - 36.5 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
BioNet 1.70.0
Routines for the functional analysis of biological networks
6 versions - Latest release: 4 months ago - 3 dependent packages - 86 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 - 403 thousand downloads total - 8 stars on GitHub - 1 maintainer
transcriptogramer 1.32.0
Transcriptional analysis based on transcriptograms
6 versions - Latest release: 4 months ago - 16.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
syntenet 1.12.0
Inference And Analysis Of Synteny Networks
10 versions - Latest release: 4 months ago - 1 dependent package - 11.5 thousand downloads total - 36 stars on GitHub - 1 maintainer
poem 1.2.0
POpulation-based Evaluation Metrics
3 versions - Latest release: 4 months ago - 2.87 thousand downloads total - 11 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: 4 months ago - 1 dependent package - 71.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
paircompviz 1.48.0
Multiple comparison test visualization
6 versions - Latest release: 4 months ago - 24.6 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 - 33.9 thousand downloads total - 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: 4 months ago - 3 dependent packages - 143 thousand downloads total - 1 maintainer
netZooR 1.14.2
A Menagerie of Methods for the Inference and Analysis of Gene Regulatory Networks
7 versions - Latest release: 2 days ago - 6.5 thousand downloads total - 113 stars on GitHub - 1 maintainer
gsean 1.30.0
Gene Set Enrichment Analysis with Networks
6 versions - Latest release: 4 months ago - 15.3 thousand downloads total - 1 maintainer
BatchQC 2.6.1
Batch Effects Quality Control Software
7 versions - Latest release: about 1 month ago - 30.4 thousand downloads total - 9 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: 4 months ago - 5.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MOGAMUN 1.20.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
6 versions - Latest release: 4 months ago - 10.2 thousand downloads total - 12 stars on GitHub - 1 maintainer
fgga 1.18.0
Hierarchical ensemble method based on factor graph
7 versions - Latest release: 4 months ago - 9.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance
6 versions - Latest release: 4 months ago - 11.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
BioNERO 1.18.0
Biological Network Reconstruction Omnibus
9 versions - Latest release: 4 months ago - 1 dependent package - 24.7 thousand downloads total - 32 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: 4 months ago - 10.7 thousand downloads total - 0 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: about 2 months ago - 7.59 thousand downloads total - 2 stars on GitHub - 1 maintainer
netSmooth 1.30.0
Network smoothing for scRNAseq
6 versions - Latest release: 4 months ago - 1 dependent package - 16.4 thousand downloads total - 28 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: 5 months ago - 3 dependent packages - 62.6 thousand downloads total - 1 maintainer
VennDetail 1.26.0
Comprehensive Visualization and Analysis of Multi-Set Intersections
6 versions - Latest release: 4 months ago - 22.5 thousand downloads total - 24 stars on GitHub - 1 maintainer
ternarynet 1.54.0
Ternary Network Estimation
6 versions - Latest release: 4 months ago - 26.1 thousand downloads total - 1 maintainer
FELLA 1.30.0
Interpretation and enrichment for metabolomics data
6 versions - Latest release: 4 months ago - 23.7 thousand downloads total - 1 maintainer
NetPathMiner 1.46.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
6 versions - Latest release: 4 months ago - 27 thousand downloads total - 9 stars on GitHub - 1 maintainer
QuaternaryProd 1.44.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
6 versions - Latest release: 4 months ago - 19 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: 4 months ago - 5 dependent packages - 75.7 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: 4 months ago - 1 dependent package - 33.8 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: 4 months ago - 13 dependent packages - 771 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: 4 months ago - 29.6 thousand downloads total - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series
6 versions - Latest release: 4 months ago - 30.4 thousand downloads total - 1 maintainer
RTNduals 1.34.1
Analysis of co-regulation and inference of 'dual regulons'
7 versions - Latest release: 14 days ago - 1 dependent package - 17.4 thousand downloads total - 2 maintainers
PPInfer 1.36.0
Inferring functionally related proteins using protein interaction networks
6 versions - Latest release: 4 months ago - 1 dependent package - 20.8 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MVCClass 1.84.0
Model-View-Controller (MVC) Classes
6 versions - Latest release: 4 months ago - 1 dependent package - 40.8 thousand downloads total - 1 maintainer
MetaboSignal 1.40.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
7 versions - Latest release: 4 months ago - 22.3 thousand downloads total - 2 maintainers
RITAN 1.34.0
Rapid Integration of Term Annotation and Network resources
6 versions - Latest release: 4 months ago - 16.1 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.68.0
Mutual Information NETworks
6 versions - Latest release: 4 months ago - 9 dependent packages - 167 thousand downloads total - 1 maintainer
RCyjs 2.32.0
Display and manipulate graphs in cytoscape.js
6 versions - Latest release: 4 months ago - 21.8 thousand downloads total - 1 maintainer
PIUMA 1.6.1
Phenotypes Identification Using Mapper from topological data Analysis
5 versions - Latest release: 16 days ago - 4.83 thousand downloads total - 5 stars on GitHub - 1 maintainer
GRaNIE 1.14.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...
6 versions - Latest release: 4 months ago - 10.4 thousand downloads total - 1 maintainer
COSNet 1.44.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
6 versions - Latest release: 4 months ago - 21.6 thousand downloads total - 1 stars on GitHub
Top 3.9% on bioconductor.org
pathview 1.50.0
a tool set for pathway based data integration and visualization
6 versions - Latest release: 4 months ago - 9 dependent packages - 697 thousand downloads total - 41 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
apComplex 2.76.0
Estimate protein complex membership using AP-MS protein data
6 versions - Latest release: 4 months ago - 53.3 thousand downloads total - 1 maintainer
netresponse 1.70.0
Functional Network Analysis
6 versions - Latest release: 4 months ago - 33.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
tidysbml 1.4.0
Extract SBML's data into dataframes
3 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 Script
6 versions - Latest release: 4 months ago - 17.4 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
BioMVCClass 1.78.0
Model-View-Controller (MVC) Classes That Use Biobase
6 versions - Latest release: 4 months ago - 43.6 thousand downloads total - 1 maintainer
mirIntegrator 1.40.0
Integrating microRNA expression into signaling pathways for pathway analysis
6 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 Networks
6 versions - Latest release: 4 months ago - 1 dependent package - 29.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
biocGraph 1.72.0
Graph examples and use cases in Bioinformatics
6 versions - Latest release: 4 months ago - 1 dependent package - 64 thousand downloads total - 1 maintainer
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy
7 versions - Latest release: 4 months ago - 26.1 thousand downloads total - 1 maintainer
ClusterFoldSimilarity 1.6.0
Calculate similarity of clusters from different single cell samples using foldchanges
4 versions - Latest release: 4 months ago - 5.28 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.78.0
Render molecular pathways
6 versions - Latest release: 4 months ago - 39 thousand downloads total - 1 maintainer
rTRMui 1.48.0
A shiny user interface for rTRM
6 versions - Latest release: 4 months ago - 24.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
CEMiTool 1.34.0
Co-expression Modules identification Tool
8 versions - Latest release: 4 months ago - 40.5 thousand downloads total - 1 maintainer
pairkat 1.16.0
PaIRKAT
6 versions - Latest release: 4 months ago - 8.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
CHRONOS 1.38.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
6 versions - Latest release: 4 months ago - 19 thousand downloads total - 1 maintainer
csdR 1.16.0
Differential gene co-expression
6 versions - Latest release: 4 months ago - 7.82 thousand downloads total - 6 stars on GitHub - 1 maintainer
BioNAR 1.12.2
Biological Network Analysis in R
11 versions - Latest release: 4 months ago - 8.39 thousand downloads total - 1 maintainer
magrene 1.12.0
Motif Analysis In Gene Regulatory Networks
6 versions - Latest release: 4 months ago - 6.87 thousand downloads total - 1 stars on GitHub - 1 maintainer
TMSig 1.4.0
Tools for Molecular Signatures
3 versions - Latest release: 4 months ago - 3.45 thousand downloads total - 4 stars on GitHub - 1 maintainer
sincell 1.42.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
6 versions - Latest release: 4 months ago - 23.6 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.30.1
Functions to Access and Control Cytoscape
8 versions - Latest release: 3 months ago - 15 dependent packages - 120 thousand downloads total - 54 stars on GitHub - 1 maintainer
Pigengene 1.35.0
Infers biological signatures from gene expression data
6 versions - Latest release: 4 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
Top 4.5% on bioconductor.org
GENIE3 1.32.0
GEne Network Inference with Ensemble of trees
6 versions - Latest release: 4 months ago - 2 dependent packages - 131 thousand downloads total - 1 maintainer
nethet 1.42.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
6 versions - Latest release: 4 months ago - 20.9 thousand downloads total - 2 maintainers
MOSClip 1.4.0
Multi Omics Survival Clip
6 versions - Latest release: 4 months ago - 3.65 thousand downloads total - 0 stars on GitHub - 1 maintainer
diffuStats 1.30.0
Diffusion scores on biological networks
6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
CBN2Path 1.0.0
"CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjun...
2 versions - Latest release: 4 months ago - 1.22 thousand downloads total - 0 stars on GitHub - 1 maintainer
RTNsurvival 1.34.1
Survival analysis using transcriptional networks inferred by the RTN package
7 versions - Latest release: 17 days ago - 16.2 thousand downloads total - 2 maintainers
OmnipathR 3.18.4
OmniPath web service client and more
11 versions - Latest release: about 2 months ago - 3 dependent packages - 65.8 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
RTN 2.34.1
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
7 versions - Latest release: 17 days ago - 3 dependent packages - 41 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAT 1.82.0
Graph Theoretic Association Tests
6 versions - Latest release: 4 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 Process
7 versions - Latest release: 4 months ago - 20.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
rScudo 1.26.0
Signature-based Clustering for Diagnostic Purposes
7 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 leaves
7 versions - Latest release: 18 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: 4 months ago - 11.8 thousand downloads total - 1 maintainer
pandaR 1.42.0
PANDA Algorithm
6 versions - Latest release: 4 months ago - 1 dependent package - 25.3 thousand downloads total - 2 maintainers
DeepPINCS 1.18.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
6 versions - Latest release: 4 months ago - 2 dependent packages - 9.47 thousand downloads total - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.76.0
Tools for manipulating GO and microarrays
6 versions - Latest release: 4 months ago - 23 dependent packages - 589 thousand downloads total - 1 maintainer
HGC 1.18.0
A fast hierarchical graph-based clustering method
6 versions - Latest release: 4 months ago - 10 thousand downloads total - 1 maintainer
splineTimeR 1.38.0
Time-course differential gene expression data analysis using spline regression models followed by...
6 versions - Latest release: 4 months ago - 19.7 thousand downloads total - 2 maintainers
iNETgrate 1.8.0
Integrates DNA methylation data with gene expression in a single gene network
6 versions - Latest release: about 2 months ago - 5.72 thousand downloads total - 65 stars on GitHub - 1 maintainer
ReactomeGraph4R 1.18.0
Interface for the Reactome Graph Database
7 versions - Latest release: 4 months ago - 4.58 thousand downloads total - 6 stars on GitHub - 1 maintainer
scGraphVerse 1.0.0
scGraphVerse: A Gene Network Analysis Package
1 version - Latest release: 5 months ago - 818 downloads total - 1 stars on GitHub - 1 maintainer
EGAD 1.38.0
Extending guilt by association by degree
6 versions - Latest release: 4 months ago - 22.1 thousand downloads total - 1 maintainer
BiGGR 1.46.0
Constraint based modeling in R using metabolic reconstruction databases
6 versions - Latest release: 4 months ago - 33.5 thousand downloads total - 2 maintainers
Top 9.8% on bioconductor.org
EGSEA 1.38.0
Ensemble of Gene Set Enrichment Analyses
7 versions - Latest release: 4 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
Related Keywords
Software 151 Network 91 GeneExpression 53 Pathways 48 Visualization 38 NetworkInference 37 SystemsBiology 33 Microarray 29 Clustering 29 NetworkEnrichment 28 GeneSetEnrichment 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 Reactome 11 BiomedicalInformatics 11 Genetics 10 GO 10 Proteomics 9 ThirdPartyClient 9 DimensionReduction 9 GeneTarget 9 DataImport 8 Annotation 8 Normalization 8 Bayesian 8 bioinformatics 7 mRNAMicroarray 6 r 6 GenePrediction 6 QualityControl 6 DataRepresentation 6 CellBiology 6 MultipleComparison 5 Preprocessing 5 PrincipalComponent 5 FunctionalGenomics 5 GeneSignaling 5 Survival 5 ATACSeq 4 GeneticVariability 4 SNP 4 GUI 4 r-package 4 GenomeWideAssociation 4 NeuralNetwork 3 TwoChannel 3 DecisionTree 3 TimeCourse 3 Infrastructure 3 MassSpectrometry 3 bioconductor 3 FeatureExtraction 3 CopyNumberVariation 2 enrichment-analysis 2 DNAMethylation 2 network-analysis 2 HiC 2 Epigenetics 2 DNASeq 2 SomaticMutation 2 CellBasedAssays 2 networks 2 ReportWriting 2 systems-biology 2 genomics 2 ChIPSeq 2 pathways 2 Phylogenetics 2 Spatial 2 BatchEffect 2 network-science 2 gene-regulatory-network 2 rstats 2 gene 1 AlternativeSplicing 1 pipeline 1 causality 1 transcriptomics 1 bioconductor-package 1 u24ca289073 1 gwas 1 snps 1 WorkflowStep 1 SequenceMatching 1 Coverage 1 co-expression 1 OneChannel 1 Systems Biology 1 BioCarta 1