bioconductor.org "GraphAndNetwork" keyword
View the packages on the bioconductor.org package registry that are tagged with the "GraphAndNetwork" keyword.
Top 1.0% on bioconductor.org
5 versions - Latest release: 5 months ago - 61 dependent packages - 1.74 million downloads total - 1 maintainer
Rgraphviz 2.52.0
Provides plotting capabilities for R graph objects5 versions - Latest release: 5 months ago - 61 dependent packages - 1.74 million downloads total - 1 maintainer
rWikiPathways 1.28.0
rWikiPathways - R client library for the WikiPathways API5 versions - Latest release: 5 months ago - 5 dependent packages - 70.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
5 versions - Latest release: 5 months ago - 49 dependent packages - 1.21 million downloads total - 1 maintainer
GSEABase 1.70.0
Gene set enrichment data structures and methods5 versions - Latest release: 5 months ago - 49 dependent packages - 1.21 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
5 versions - Latest release: 5 months ago - 33 dependent packages - 1.72 million downloads total - 1 maintainer
RBGL 1.84.0
An interface to the BOOST graph library5 versions - Latest release: 5 months ago - 33 dependent packages - 1.72 million downloads total - 1 maintainer
PhenoGeneRanker 1.16.0
PhenoGeneRanker: A gene and phenotype prioritization tool5 versions - Latest release: 4 months ago - 6.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 0.7% on bioconductor.org
6 versions - Latest release: 5 months ago - 101 dependent packages - 3.1 million downloads total - 1 maintainer
graph 1.86.0
graph: A package to handle graph data structures6 versions - Latest release: 5 months ago - 101 dependent packages - 3.1 million downloads total - 1 maintainer
BioNetStat 1.24.0 removed
Biological Network Analysis3 versions - Latest release: over 1 year ago - 9.35 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
6 versions - Latest release: 5 months ago - 4 dependent packages - 58.1 thousand downloads total - 1 maintainer
RedeR 3.4.0
Interactive visualization and manipulation of nested networks6 versions - Latest release: 5 months ago - 4 dependent packages - 58.1 thousand downloads total - 1 maintainer
HGC 1.16.0
A fast hierarchical graph-based clustering method5 versions - Latest release: 4 months ago - 7.6 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
5 versions - Latest release: 4 months ago - 49.8 thousand downloads total - 1 maintainer
apComplex 2.74.0
Estimate protein complex membership using AP-MS protein data5 versions - Latest release: 4 months ago - 49.8 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 1 maintainer
NCIgraph 1.56.0
Pathways from the NCI Pathways Database5 versions - Latest release: 4 months ago - 1 dependent package - 1 maintainer
Top 4.6% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 62.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data5 versions - Latest release: 4 months ago - 1 dependent package - 62.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
5 versions - Latest release: 5 months ago - 3 dependent packages - 58.3 thousand downloads total - 1 maintainer
hypergraph 1.80.0
A package providing hypergraph data structures5 versions - Latest release: 5 months ago - 3 dependent packages - 58.3 thousand downloads total - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions14 versions - Latest release: 2 months ago - 12.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
COSNet 1.42.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings5 versions - Latest release: 4 months ago - 19.4 thousand downloads total - 1 stars on GitHub
CausalR 1.40.0
Causal network analysis methods5 versions - Latest release: 4 months ago - 18.2 thousand downloads total - 2 maintainers
glmSparseNet 1.26.0
Network Centrality Metrics for Elastic-Net Regularized Models6 versions - Latest release: 4 months ago - 105 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
goProfiles 1.70.0
goProfiles: an R package for the statistical analysis of functional profiles5 versions - Latest release: 4 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions5 versions - Latest release: 4 months ago - 8.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
SGCP 1.8.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...7 versions - Latest release: 5 months ago - 5.87 thousand downloads total - 2 stars on GitHub - 1 maintainer
sparsenetgls 1.26.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...5 versions - Latest release: 4 months ago - 9.67 thousand downloads total - 1 maintainer
hipathia 3.8.0
HiPathia: High-throughput Pathway Analysis5 versions - Latest release: 4 months ago - 1 maintainer
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization5 versions - Latest release: 5 months ago - 24 thousand downloads total - 9 stars on GitHub - 1 maintainer
SBGNview 1.22.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"5 versions - Latest release: 4 months ago - 14.5 thousand downloads total - 28 stars on GitHub - 1 maintainer
martini 1.28.0
GWAS Incorporating Networks5 versions - Latest release: 4 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data5 versions - Latest release: 4 months ago - 6.45 thousand downloads total - 4 stars on GitHub - 1 maintainer
ceRNAnetsim 1.20.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)6 versions - Latest release: 4 months ago - 8.05 thousand downloads total - 5 stars on GitHub - 1 maintainer
GRaNIE 1.12.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...5 versions - Latest release: 4 months ago - 8.31 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
5 versions - Latest release: 4 months ago - 34 thousand downloads total - 1 maintainer
GraphAlignment 1.72.0
GraphAlignment5 versions - Latest release: 4 months ago - 34 thousand downloads total - 1 maintainer
sincell 1.40.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data5 versions - Latest release: 4 months ago - 21 thousand downloads total - 1 maintainer
pandaR 1.40.0
PANDA Algorithm5 versions - Latest release: 4 months ago - 1 dependent package - 22.5 thousand downloads total - 2 maintainers
Top 4.5% on bioconductor.org
5 versions - Latest release: 5 months ago - 2 dependent packages - 107 thousand downloads total - 1 maintainer
GENIE3 1.30.0
GEne Network Inference with Ensemble of trees5 versions - Latest release: 5 months ago - 2 dependent packages - 107 thousand downloads total - 1 maintainer
mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis5 versions - Latest release: 5 months ago - 17.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
RGraph2js 1.36.0
Convert a Graph into a D3js Script5 versions - Latest release: 4 months ago - 15 thousand downloads total - 1 maintainer
nethet 1.40.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity5 versions - Latest release: 4 months ago - 18.5 thousand downloads total - 2 maintainers
EGAD 1.36.0
Extending guilt by association by degree5 versions - Latest release: 4 months ago - 18.5 thousand downloads total - 1 maintainer
CEMiTool 1.32.0
Co-expression Modules identification Tool6 versions - Latest release: 4 months ago - 34.8 thousand downloads total - 1 maintainer
CHRONOS 1.36.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis5 versions - Latest release: 4 months ago - 16.8 thousand downloads total - 1 maintainer
epiregulon.extra 1.4.0
Companion package to epiregulon with additional plotting, differential and graph functions6 versions - Latest release: 4 months ago - 3.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
tidysbml 1.2.0
Extract SBML's data into dataframes2 versions - Latest release: 4 months ago - 2.27 thousand downloads total - 1 stars on GitHub - 1 maintainer
fobitools 1.16.0
Tools for Manipulating the FOBI Ontology5 versions - Latest release: 4 months ago - 7.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
dcanr 1.24.0
Differential co-expression/association network analysis5 versions - Latest release: 5 months ago - 1 dependent package - 14.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
PathoStat 1.34.0
PathoStat Statistical Microbiome Analysis Package5 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 8 stars on GitHub - 2 maintainers
magrene 1.10.0
Motif Analysis In Gene Regulatory Networks5 versions - Latest release: 4 months ago - 5.32 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 38.2 thousand downloads total - 1 maintainer
MVCClass 1.82.0
Model-View-Controller (MVC) Classes5 versions - Latest release: 4 months ago - 1 dependent package - 38.2 thousand downloads total - 1 maintainer
ternarynet 1.52.0
Ternary Network Estimation5 versions - Latest release: 4 months ago - 23.9 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 120 thousand downloads total - 1 maintainer
SPIA 2.60.0
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation a...5 versions - Latest release: 4 months ago - 3 dependent packages - 120 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses6 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
goSorensen 1.10.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)5 versions - Latest release: 4 months ago - 5.66 thousand downloads total - 1 maintainer
netresponse 1.68.0
Functional Network Analysis5 versions - Latest release: 5 months ago - 30.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
BioNAR 1.10.0
Biological Network Analysis in R10 versions - Latest release: 4 months ago - 6.2 thousand downloads total - 1 maintainer
RTNduals 1.32.0
Analysis of co-regulation and inference of 'dual regulons'5 versions - Latest release: 4 months ago - 1 dependent package - 15 thousand downloads total - 2 maintainers
Pigengene 1.34.0
Infers biological signatures from gene expression data5 versions - Latest release: 4 months ago - 1 dependent package - 19.4 thousand downloads total - 1 maintainer
GmicR 1.22.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...5 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 1 maintainer
R3CPET 1.40.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process6 versions - Latest release: 4 months ago - 17.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks5 versions - Latest release: 5 months ago - 1 dependent package - 26 thousand downloads total - 3 stars on GitHub - 1 maintainer
fgga 1.16.0
Hierarchical ensemble method based on factor graph6 versions - Latest release: 5 months ago - 7.42 thousand downloads total - 3 stars on GitHub - 1 maintainer
CIMICE 1.16.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution5 versions - Latest release: 4 months ago - 7.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 74.1 thousand downloads total - 1 maintainer
BioNet 1.68.0
Routines for the functional analysis of biological networks5 versions - Latest release: 4 months ago - 3 dependent packages - 74.1 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 36 thousand downloads total - 1 maintainer
RTN 2.32.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons5 versions - Latest release: 4 months ago - 3 dependent packages - 36 thousand downloads total - 1 maintainer
PPInfer 1.34.0
Inferring functionally related proteins using protein interaction networks5 versions - Latest release: 4 months ago - 1 dependent package - 18 thousand downloads total - 1 maintainer
iNETgrate 1.6.0
Integrates DNA methylation data with gene expression in a single gene network4 versions - Latest release: 4 months ago - 4.77 thousand downloads total - 65 stars on GitHub - 1 maintainer
PANR 1.54.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...5 versions - Latest release: 4 months ago - 27.2 thousand downloads total - 1 maintainer
RTNsurvival 1.32.0
Survival analysis using transcriptional networks inferred by the RTN package5 versions - Latest release: 4 months ago - 13.7 thousand downloads total - 2 maintainers
paircompviz 1.46.0
Multiple comparison test visualization5 versions - Latest release: 4 months ago - 22.1 thousand downloads total - 1 maintainer
QuaternaryProd 1.42.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs5 versions - Latest release: 4 months ago - 16.9 thousand downloads total - 1 maintainer
RCyjs 2.30.0
Display and manipulate graphs in cytoscape.js5 versions - Latest release: 4 months ago - 18.8 thousand downloads total - 1 maintainer
GeneNetworkBuilder 1.50.0
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-s...5 versions - Latest release: 4 months ago - 29.7 thousand downloads total - 1 maintainer
MetaboSignal 1.38.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways6 versions - Latest release: 4 months ago - 19.4 thousand downloads total - 2 maintainers
TreeAndLeaf 1.20.0
Displaying binary trees with focus on dendrogram leaves5 versions - Latest release: 4 months ago - 1 dependent package - 12.5 thousand downloads total - 1 maintainer
ClusterFoldSimilarity 1.4.0
Calculate similarity of clusters from different single cell samples using foldchanges3 versions - Latest release: 5 months ago - 3.77 thousand downloads total - 1 maintainer
rTRMui 1.46.0
A shiny user interface for rTRM5 versions - Latest release: 5 months ago - 21.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
transcriptogramer 1.30.0
Transcriptional analysis based on transcriptograms5 versions - Latest release: 5 months ago - 13.6 thousand downloads total - 4 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: 4 months ago - 7.81 thousand downloads total - 12 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons5 versions - Latest release: 4 months ago - 27.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
netSmooth 1.28.0
Network smoothing for scRNAseq5 versions - Latest release: 5 months ago - 1 dependent package - 13.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
TRONCO 2.40.0
TRONCO, an R package for TRanslational ONCOlogy5 versions - Latest release: 4 months ago - 22 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
5 versions - Latest release: 4 months ago - 9 dependent packages - 140 thousand downloads total - 1 maintainer
minet 3.66.0
Mutual Information NETworks5 versions - Latest release: 4 months ago - 9 dependent packages - 140 thousand downloads total - 1 maintainer
PIUMA 1.4.0
Phenotypes Identification Using Mapper from topological data Analysis3 versions - Latest release: 4 months ago - 3.66 thousand downloads total - 5 stars on GitHub - 1 maintainer
BatchQC 2.4.0
Batch Effects Quality Control Software5 versions - Latest release: 4 months ago - 26.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
dce 1.13.0
Pathway Enrichment Based on Differential Causal Effects4 versions - Latest release: 10 months ago - 6.67 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
5 versions - Latest release: 4 months ago - 9 dependent packages - 607 thousand downloads total - 41 stars on GitHub - 1 maintainer
pathview 1.48.0
a tool set for pathway based data integration and visualization5 versions - Latest release: 4 months ago - 9 dependent packages - 607 thousand downloads total - 41 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
5 versions - Latest release: 4 months ago - 35.7 thousand downloads total - 1 maintainer
pathRender 1.76.0
Render molecular pathways5 versions - Latest release: 4 months ago - 35.7 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
5 versions - Latest release: 4 months ago - 35.1 thousand downloads total - 1 maintainer
SBMLR 2.4.0
SBML-R Interface and Analysis Tools5 versions - Latest release: 4 months ago - 35.1 thousand downloads total - 1 maintainer
Top 9.7% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 31.4 thousand downloads total - 1 maintainer
DEGraph 1.60.0
Two-sample tests on a graph5 versions - Latest release: 4 months ago - 1 dependent package - 31.4 thousand downloads total - 1 maintainer
PanViz 1.10.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data5 versions - Latest release: 4 months ago - 3.36 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
5 versions - Latest release: 4 months ago - 35.9 thousand downloads total - 1 maintainer
GraphAT 1.80.0
Graph Theoretic Association Tests5 versions - Latest release: 4 months ago - 35.9 thousand downloads total - 1 maintainer
splineTimeR 1.36.0
Time-course differential gene expression data analysis using spline regression models followed by...5 versions - Latest release: 4 months ago - 17.4 thousand downloads total - 2 maintainers
DART 1.56.0
Denoising Algorithm based on Relevance network Topology5 versions - Latest release: 4 months ago - 30.1 thousand downloads total - 1 maintainer
KEGGlincs 1.34.0
Visualize all edges within a KEGG pathway and overlay LINCS data5 versions - Latest release: 4 months ago - 16 thousand downloads total - 2 maintainers
RITAN 1.32.0
Rapid Integration of Term Annotation and Network resources5 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 1 maintainer
airpart 1.16.0
Differential cell-type-specific allelic imbalance5 versions - Latest release: 4 months ago - 9.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
csdR 1.14.0
Differential gene co-expression5 versions - Latest release: 4 months ago - 6.3 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
5 versions - Latest release: 5 months ago - 23 dependent packages - 536 thousand downloads total - 1 maintainer
GOstats 2.74.0
Tools for manipulating GO and microarrays5 versions - Latest release: 5 months ago - 23 dependent packages - 536 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 4 months ago - 13 dependent packages - 653 thousand downloads total - 1 maintainer
KEGGgraph 1.68.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor5 versions - Latest release: 4 months ago - 13 dependent packages - 653 thousand downloads total - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more7 versions - Latest release: 4 months ago - 3 dependent packages - 46.3 thousand downloads total - 1 maintainer
MOSClip 1.2.2
Multi Omics Survival Clip4 versions - Latest release: 3 months ago - 2.11 thousand downloads total - 0 stars on GitHub - 1 maintainer
GRENITS 1.60.0
Gene Regulatory Network Inference Using Time Series5 versions - Latest release: 4 months ago - 28 thousand downloads total - 1 maintainer
Related Keywords
Software
149
Network
90
GeneExpression
53
Pathways
46
Visualization
36
NetworkInference
36
SystemsBiology
32
Clustering
29
Microarray
29
GeneSetEnrichment
27
NetworkEnrichment
27
RNASeq
25
DifferentialExpression
25
KEGG
22
ImmunoOncology
21
GeneRegulation
16
Transcription
16
Transcriptomics
16
Metabolomics
14
Sequencing
14
Regression
13
Classification
12
StatisticalMethod
12
BiomedicalInformatics
11
Genetics
10
SingleCell
10
GO
10
Reactome
10
Proteomics
9
ThirdPartyClient
9
DimensionReduction
9
GeneTarget
9
Annotation
8
DataImport
8
Normalization
8
Bayesian
7
bioinformatics
7
mRNAMicroarray
6
GenePrediction
6
DataRepresentation
6
CellBiology
6
r
6
QualityControl
6
Preprocessing
5
GeneSignaling
5
FunctionalGenomics
5
MultipleComparison
5
PrincipalComponent
5
Survival
5
GUI
4
GenomeWideAssociation
4
r-package
4
Infrastructure
4
GeneticVariability
4
SNP
4
ATACSeq
4
TwoChannel
3
bioconductor
3
DecisionTree
3
TimeCourse
3
FeatureExtraction
3
NeuralNetwork
3
MassSpectrometry
3
ReportWriting
2
gene-regulatory-network
2
network-science
2
rstats
2
systems-biology
2
CellBasedAssays
2
network-analysis
2
DNASeq
2
genomics
2
HiC
2
CopyNumberVariation
2
BatchEffect
2
SomaticMutation
2
Spatial
2
networks
2
pathways
2
Epigenetics
2
ChIPSeq
2
DNAMethylation
2
Phylogenetics
2
enrichment-analysis
2
ggplot2
1
FlowCytometry
1
plotting
1
shiny
1
transcription-factors
1
ComparativeGenomics
1
WholeGenome
1
Coverage
1
Systems Biology
1
Pathway
1
TranscriptomeVariant
1
data-access
1
causality
1
single-cell
1
cran
1
core-services
1