bioconductor.org "GraphAndNetwork" keyword
Top 1.4% on bioconductor.org
7 versions - Latest release: 6 months ago - 49 dependent packages - 1.42 million downloads total - 1 maintainer
GSEABase 1.72.0
Gene set enrichment data structures and methods7 versions - Latest release: 6 months ago - 49 dependent packages - 1.42 million downloads total - 1 maintainer
rTRMui 1.48.0
A shiny user interface for rTRM6 versions - Latest release: 5 months ago - 25.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
mirIntegrator 1.40.0
Integrating microRNA expression into signaling pathways for pathway analysis6 versions - Latest release: 5 months ago - 20.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
6 versions - Latest release: 5 months ago - 33 dependent packages - 1.94 million downloads total - 1 maintainer
RBGL 1.86.0
An interface to the BOOST graph library6 versions - Latest release: 5 months ago - 33 dependent packages - 1.94 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
6 versions - Latest release: 6 months ago - 61 dependent packages - 1.95 million downloads total - 1 maintainer
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects6 versions - Latest release: 6 months ago - 61 dependent packages - 1.95 million downloads total - 1 maintainer
csdR 1.16.0
Differential gene co-expression6 versions - Latest release: 5 months ago - 8.3 thousand downloads total - 6 stars on GitHub - 1 maintainer
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series6 versions - Latest release: 5 months ago - 31.1 thousand downloads total - 1 maintainer
TMSig 1.4.0
Tools for Molecular Signatures3 versions - Latest release: 5 months ago - 3.89 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
6 versions - Latest release: 5 months ago - 44.7 thousand downloads total - 1 maintainer
BioMVCClass 1.78.0
Model-View-Controller (MVC) Classes That Use Biobase6 versions - Latest release: 5 months ago - 44.7 thousand downloads total - 1 maintainer
ClusterFoldSimilarity 1.6.0
Calculate similarity of clusters from different single cell samples using foldchanges4 versions - Latest release: 5 months ago - 5.71 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
8 versions - Latest release: 4 months ago - 101 dependent packages - 3.55 million downloads total - 1 maintainer
graph 1.88.1
graph: A package to handle graph data structures8 versions - Latest release: 4 months ago - 101 dependent packages - 3.55 million downloads total - 1 maintainer
Top 9.2% on bioconductor.org
6 versions - Latest release: 5 months ago - 40.1 thousand downloads total - 1 maintainer
GraphAT 1.82.0
Graph Theoretic Association Tests6 versions - Latest release: 5 months ago - 40.1 thousand downloads total - 1 maintainer
fobitools 1.18.0
Tools for Manipulating the FOBI Ontology6 versions - Latest release: 5 months ago - 9.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
CEMiTool 1.34.0
Co-expression Modules identification Tool8 versions - Latest release: 5 months ago - 41.3 thousand downloads total - 1 maintainer
CHRONOS 1.38.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis6 versions - Latest release: 5 months ago - 19.7 thousand downloads total - 1 maintainer
netresponse 1.70.0
Functional Network Analysis6 versions - Latest release: 5 months ago - 34.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
rScudo 1.26.0
Signature-based Clustering for Diagnostic Purposes7 versions - Latest release: 5 months ago - 13 thousand downloads total - 4 stars on GitHub - 1 maintainer
RTNduals 1.34.1
Analysis of co-regulation and inference of 'dual regulons'7 versions - Latest release: about 1 month ago - 1 dependent package - 18.2 thousand downloads total - 2 maintainers
RGraph2js 1.38.0
Convert a Graph into a D3js Script6 versions - Latest release: 5 months ago - 18.1 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: 5 months ago - 11.1 thousand downloads total - 1 maintainer
pairkat 1.16.0
PaIRKAT6 versions - Latest release: 5 months ago - 8.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
6 versions - Latest release: 5 months ago - 23 dependent packages - 594 thousand downloads total - 1 maintainer
GOstats 2.76.0
Tools for manipulating GO and microarrays6 versions - Latest release: 5 months ago - 23 dependent packages - 594 thousand downloads total - 1 maintainer
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy7 versions - Latest release: 5 months ago - 26.9 thousand downloads total - 1 maintainer
PIUMA 1.6.1
Phenotypes Identification Using Mapper from topological data Analysis5 versions - Latest release: about 1 month ago - 5.25 thousand downloads total - 5 stars on GitHub - 1 maintainer
rTRM 1.48.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks6 versions - Latest release: 5 months ago - 1 dependent package - 30.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
tidysbml 1.4.0
Extract SBML's data into dataframes3 versions - Latest release: 5 months ago - 3.96 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 Process7 versions - Latest release: 5 months ago - 21 thousand downloads total - 3 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: 5 months ago - 22.3 thousand downloads total - 1 stars on GitHub
magrene 1.12.0
Motif Analysis In Gene Regulatory Networks6 versions - Latest release: 5 months ago - 7.32 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
6 versions - Latest release: 5 months ago - 9 dependent packages - 169 thousand downloads total - 1 maintainer
minet 3.68.0
Mutual Information NETworks6 versions - Latest release: 5 months ago - 9 dependent packages - 169 thousand downloads total - 1 maintainer
Pigengene 1.36.0
Infers biological signatures from gene expression data7 versions - Latest release: 6 days ago - 1 dependent package - 22.2 thousand downloads total - 1 maintainer
nethet 1.42.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity6 versions - Latest release: 5 months ago - 21.7 thousand downloads total - 2 maintainers
RCyjs 2.32.0
Display and manipulate graphs in cytoscape.js6 versions - Latest release: 5 months ago - 22.5 thousand downloads total - 1 maintainer
Top 6.9% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 65.1 thousand downloads total - 1 maintainer
biocGraph 1.72.0
Graph examples and use cases in Bioinformatics6 versions - Latest release: 5 months ago - 1 dependent package - 65.1 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: 5 months ago - 19.7 thousand downloads total - 2 maintainers
PPInfer 1.36.0
Inferring functionally related proteins using protein interaction networks6 versions - Latest release: 5 months ago - 1 dependent package - 21.5 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
8 versions - Latest release: 4 months ago - 15 dependent packages - 122 thousand downloads total - 54 stars on GitHub - 1 maintainer
RCy3 2.30.1
Functions to Access and Control Cytoscape8 versions - Latest release: 4 months ago - 15 dependent packages - 122 thousand downloads total - 54 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
6 versions - Latest release: 5 months ago - 9 dependent packages - 706 thousand downloads total - 41 stars on GitHub - 1 maintainer
pathview 1.50.0
a tool set for pathway based data integration and visualization6 versions - Latest release: 5 months ago - 9 dependent packages - 706 thousand downloads total - 41 stars on GitHub - 1 maintainer
ceRNAnetsim 1.22.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)7 versions - Latest release: 5 months ago - 10.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
RITAN 1.34.0
Rapid Integration of Term Annotation and Network resources6 versions - Latest release: 5 months ago - 16.7 thousand downloads total - 1 maintainer
MOSClip 1.4.0
Multi Omics Survival Clip6 versions - Latest release: 5 months ago - 4.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.3% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 41.9 thousand downloads total - 1 maintainer
MVCClass 1.84.0
Model-View-Controller (MVC) Classes6 versions - Latest release: 5 months ago - 1 dependent package - 41.9 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
6 versions - Latest release: 5 months ago - 2 dependent packages - 134 thousand downloads total - 1 maintainer
GENIE3 1.32.0
GEne Network Inference with Ensemble of trees6 versions - Latest release: 5 months ago - 2 dependent packages - 134 thousand downloads total - 1 maintainer
BioNAR 1.12.2
Biological Network Analysis in R11 versions - Latest release: 5 months ago - 8.86 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
6 versions - Latest release: 5 months ago - 54.3 thousand downloads total - 1 maintainer
apComplex 2.76.0
Estimate protein complex membership using AP-MS protein data6 versions - Latest release: 5 months ago - 54.3 thousand downloads total - 1 maintainer
KEGGlincs 1.36.0
Visualize all edges within a KEGG pathway and overlay LINCS data6 versions - Latest release: 5 months ago - 19.1 thousand downloads total - 2 maintainers
goSorensen 1.12.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)6 versions - Latest release: 5 months ago - 7.75 thousand downloads total - 1 maintainer
sincell 1.42.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data6 versions - Latest release: 5 months ago - 24.4 thousand downloads total - 1 maintainer
GSEABenchmarkeR 1.30.0
Reproducible GSEA Benchmarking7 versions - Latest release: 5 months ago - 2 dependent packages - 19.2 thousand downloads total - 13 stars on GitHub - 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: 5 months ago - 12.4 thousand downloads total - 1 maintainer
diffuStats 1.30.0
Diffusion scores on biological networks6 versions - Latest release: 5 months ago - 17.7 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 43 thousand downloads total - 1 maintainer
hyperdraw 1.62.0
Visualizing Hypergaphs6 versions - Latest release: 5 months ago - 1 dependent package - 43 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
7 versions - Latest release: about 1 month ago - 3 dependent packages - 42.1 thousand downloads total - 1 maintainer
RTN 2.34.1
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons7 versions - Latest release: about 1 month ago - 3 dependent packages - 42.1 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 - 1.49 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: 2 months ago - 6.27 thousand downloads total - 65 stars on GitHub - 1 maintainer
pandaR 1.42.0
PANDA Algorithm6 versions - Latest release: 5 months ago - 1 dependent package - 26.2 thousand downloads total - 2 maintainers
BiGGR 1.46.0
Constraint based modeling in R using metabolic reconstruction databases6 versions - Latest release: 5 months ago - 33.9 thousand downloads total - 2 maintainers
GWENA 1.20.0
Pipeline for augmented co-expression analysis6 versions - Latest release: 5 months ago - 16.7 thousand downloads total - 18 stars on GitHub - 1 maintainer
TreeAndLeaf 1.22.2
Displaying binary trees with focus on dendrogram leaves7 versions - Latest release: about 1 month ago - 1 dependent package - 15.7 thousand downloads total - 1 maintainer
HGC 1.18.0
A fast hierarchical graph-based clustering method6 versions - Latest release: 5 months ago - 10.5 thousand downloads total - 1 maintainer
ANF 1.32.0
Affinity Network Fusion for Complex Patient Clustering7 versions - Latest release: 5 months ago - 18.5 thousand downloads total - 1 maintainer
DeepPINCS 1.18.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning6 versions - Latest release: 5 months ago - 2 dependent packages - 10 thousand downloads total - 1 maintainer
EGAD 1.38.0
Extending guilt by association by degree6 versions - Latest release: 5 months ago - 22.7 thousand downloads total - 1 maintainer
DART 1.58.0
Denoising Algorithm based on Relevance network Topology6 versions - Latest release: 5 months ago - 33.5 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: 5 months ago - 20.4 thousand downloads total - 2 maintainers
ReactomeGraph4R 1.18.0
Interface for the Reactome Graph Database7 versions - Latest release: 5 months ago - 4.74 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 41.5 thousand downloads total - 1 maintainer
EGSEA 1.38.0
Ensemble of Gene Set Enrichment Analyses7 versions - Latest release: 5 months ago - 1 dependent package - 41.5 thousand downloads total - 1 maintainer
scGraphVerse 1.0.0
scGraphVerse: A Gene Network Analysis Package1 version - Latest release: 5 months ago - 1.09 thousand downloads total - 1 stars on GitHub - 1 maintainer
martini 1.30.0
GWAS Incorporating Networks6 versions - Latest release: 5 months ago - 15.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
netboost 2.18.1
Network Analysis Supported by Boosting7 versions - Latest release: 2 months ago - 11.4 thousand downloads total - 1 maintainer
ibh 1.58.0
Interaction Based Homogeneity for Evaluating Gene Lists6 versions - Latest release: 5 months ago - 30.1 thousand downloads total - 1 maintainer
IMMAN 1.30.0
Interlog protein network reconstruction by Mapping and Mining ANalysis6 versions - Latest release: 5 months ago - 14.5 thousand downloads total - 1 maintainer
GeneNetworkBuilder 1.52.0
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-s...6 versions - Latest release: 5 months ago - 33.7 thousand downloads total - 1 maintainer
spatialHeatmap 2.16.3
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions16 versions - Latest release: 2 months ago - 15.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
rWikiPathways 1.30.0
rWikiPathways - R client library for the WikiPathways API6 versions - Latest release: 5 months ago - 5 dependent packages - 78.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
CIMICE 1.18.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution6 versions - Latest release: 5 months ago - 9.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
CausalR 1.42.0
Causal network analysis methods6 versions - Latest release: 5 months ago - 21 thousand downloads total - 2 maintainers
Top 7.8% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 54.9 thousand downloads total - 1 maintainer
keggorthology 2.62.0
graph support for KO, KEGG Orthology6 versions - Latest release: 5 months ago - 1 dependent package - 54.9 thousand downloads total - 1 maintainer
plotGrouper 1.28.0
Shiny app GUI wrapper for ggplot with built-in statistical analysis6 versions - Latest release: 5 months ago - 12.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
Rigraphlib 1.2.0
igraph library as an R package2 versions - Latest release: 4 months ago - 18 thousand downloads total - 1 stars on GitHub - 1 maintainer
SBGNview 1.24.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"6 versions - Latest release: 5 months ago - 17.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
sparsenetgls 1.28.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...6 versions - Latest release: 5 months ago - 11.8 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 54.1 thousand downloads total - 1 maintainer
goProfiles 1.72.0
goProfiles: an R package for the statistical analysis of functional profiles6 versions - Latest release: 5 months ago - 1 dependent package - 54.1 thousand downloads total - 1 maintainer
glmSparseNet 1.28.0
Network Centrality Metrics for Elastic-Net Regularized Models7 versions - Latest release: 5 months ago - 107 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.9% on bioconductor.org
6 versions - Latest release: 5 months ago - 3 dependent packages - 64.8 thousand downloads total - 1 maintainer
rsbml 2.68.0
R support for SBML, using libsbml6 versions - Latest release: 5 months ago - 3 dependent packages - 64.8 thousand downloads total - 1 maintainer
hipathia 3.9.0
HiPathia: High-throughput Pathway Analysis6 versions - Latest release: 5 months ago - 20.3 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.18.0
PhenoGeneRanker: A gene and phenotype prioritization tool6 versions - Latest release: 5 months ago - 7.89 thousand downloads total - 1 maintainer
dcanr 1.26.0
Differential co-expression/association network analysis6 versions - Latest release: 5 months ago - 1 dependent package - 18.6 thousand downloads total - 6 stars on GitHub - 1 maintainer
spqn 1.22.0
Spatial quantile normalization6 versions - Latest release: 5 months ago - 10.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
8 versions - Latest release: about 2 months ago - 4 dependent packages - 64.7 thousand downloads total - 1 maintainer
RedeR 3.6.2
Interactive visualization and manipulation of nested networks8 versions - Latest release: about 2 months ago - 4 dependent packages - 64.7 thousand downloads total - 1 maintainer
Pedixplorer 1.6.0
Pedigree Functions4 versions - Latest release: 5 months ago - 5.81 thousand downloads total - 0 stars on GitHub - 1 maintainer
KBoost 1.18.0
Inference of gene regulatory networks from gene expression data6 versions - Latest release: 5 months ago - 8.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
PathoStat 1.36.0
PathoStat Statistical Microbiome Analysis Package6 versions - Latest release: 5 months ago - 19.8 thousand downloads total - 8 stars on GitHub - 2 maintainers
wppi 1.18.0
Weighting protein-protein interactions7 versions - Latest release: 4 months ago - 11.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
6 versions - Latest release: 5 months ago - 38.3 thousand downloads total - 1 maintainer
SBMLR 2.6.0
SBML-R Interface and Analysis Tools6 versions - Latest release: 5 months ago - 38.3 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
6 versions - Latest release: 5 months ago - 36.5 thousand downloads total - 1 maintainer
GraphAlignment 1.74.0
GraphAlignment6 versions - Latest release: 5 months ago - 36.5 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
6 versions - Latest release: 5 months ago - 3 dependent packages - 86 thousand downloads total - 1 maintainer
BioNet 1.70.0
Routines for the functional analysis of biological networks6 versions - Latest release: 5 months ago - 3 dependent packages - 86 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
6 versions - Latest release: 5 months ago - 11 dependent packages - 403 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.56.0
GRAPH Interaction from pathway Topological Environment6 versions - Latest release: 5 months ago - 11 dependent packages - 403 thousand downloads total - 8 stars on GitHub - 1 maintainer
transcriptogramer 1.32.0
Transcriptional analysis based on transcriptograms6 versions - Latest release: 5 months ago - 16.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
syntenet 1.12.0
Inference And Analysis Of Synteny Networks10 versions - Latest release: 5 months ago - 1 dependent package - 11.5 thousand downloads total - 36 stars on GitHub - 1 maintainer
Related Keywords
Software
151
Network
91
GeneExpression
53
Pathways
48
Visualization
38
NetworkInference
37
SystemsBiology
33
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
Proteomics
9
ThirdPartyClient
9
DimensionReduction
9
GeneTarget
9
DataImport
8
Bayesian
8
Annotation
8
Normalization
8
bioinformatics
7
QualityControl
6
GenePrediction
6
r
6
DataRepresentation
6
CellBiology
6
mRNAMicroarray
6
MultipleComparison
5
PrincipalComponent
5
Survival
5
Preprocessing
5
GeneSignaling
5
FunctionalGenomics
5
GeneticVariability
4
r-package
4
SNP
4
ATACSeq
4
GenomeWideAssociation
4
GUI
4
TimeCourse
3
DecisionTree
3
NeuralNetwork
3
TwoChannel
3
bioconductor
3
MassSpectrometry
3
FeatureExtraction
3
Infrastructure
3
network-analysis
2
enrichment-analysis
2
Phylogenetics
2
BatchEffect
2
genomics
2
pathways
2
DNAMethylation
2
Spatial
2
CopyNumberVariation
2
rstats
2
network-science
2
systems-biology
2
gene-regulatory-network
2
networks
2
ChIPSeq
2
Epigenetics
2
ReportWriting
2
DNASeq
2
CellBasedAssays
2
HiC
2
SomaticMutation
2
evolutionary-genomics
1
comparative-genomics
1
phylogenomics
1
WholeGenome
1
ComparativeGenomics
1
pathway-analysis
1
mirror
1
random-walk-with-restart
1
ppi-networks
1
plotting
1
shiny
1
omnipath
1
human-phenotype-ontology
1
gene-prioritization
1
gene-ontology
1
PatternLogic
1