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

bioconductor.org "GraphAndNetwork" keyword

OmnipathR 4.0.0
OmniPath web service client and more
13 versions - Latest release: 3 months ago - 3 dependent packages - 87.2 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.56.0
Provides plotting capabilities for R graph objects
7 versions - Latest release: 4 months ago - 61 dependent packages - 2.02 million downloads total - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.42.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
8 versions - Latest release: 2 months ago - 5 dependent packages - 83.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
transcriptogramer 1.34.0
Transcriptional analysis based on transcriptograms
7 versions - Latest release: about 2 months ago - 20.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
magrene 1.14.0
Motif Analysis In Gene Regulatory Networks
7 versions - Latest release: 3 months ago - 9.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
MOGAMUN 1.22.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
7 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
ANF 1.34.0
Affinity Network Fusion for Complex Patient Clustering
8 versions - Latest release: 4 months ago - 21.1 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.88.0
An interface to the BOOST graph library
7 versions - Latest release: 4 months ago - 33 dependent packages - 2.01 million downloads total - 1 maintainer
KBoost 1.20.0
Inference of gene regulatory networks from gene expression data
7 versions - Latest release: 2 months ago - 9.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.32.0
Functions to Access and Control Cytoscape
9 versions - Latest release: 3 months ago - 15 dependent packages - 129 thousand downloads total - 59 stars on GitHub - 1 maintainer
sincell 1.44.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
7 versions - Latest release: 3 months ago - 27 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
SBMLR 2.8.0
SBML-R Interface and Analysis Tools
7 versions - Latest release: 3 months ago - 41.7 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.8.1
Interactive visualization and manipulation of nested networks
10 versions - Latest release: 3 days ago - 4 dependent packages - 69.5 thousand downloads total - 1 maintainer
tidysbml 1.6.0
Extract SBML's data into dataframes
4 versions - Latest release: 3 months ago - 5.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
CEMiTool 1.36.0
Co-expression Modules identification Tool
9 versions - Latest release: 3 months ago - 44.4 thousand downloads total - 1 maintainer
GWENA 1.22.0
Pipeline for augmented co-expression analysis
7 versions - Latest release: 3 months ago - 19.2 thousand downloads total - 18 stars on GitHub - 1 maintainer
CausalR 1.44.0
Causal network analysis methods
7 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 2 maintainers
Top 9.0% on bioconductor.org
RTN 2.36.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
8 versions - Latest release: 3 months ago - 3 dependent packages - 45.3 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAT 1.84.0
Graph Theoretic Association Tests
7 versions - Latest release: 3 months ago - 42.9 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAlignment 1.76.0
GraphAlignment
7 versions - Latest release: 3 months ago - 39 thousand downloads total - 1 maintainer
Rigraphlib 1.4.0
igraph library as an R package
3 versions - Latest release: 3 months ago - 33.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
MAGAR 1.20.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
7 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
BioMVCClass 1.80.0
Model-View-Controller (MVC) Classes That Use Biobase
7 versions - Latest release: 3 months ago - 47.1 thousand downloads total - 1 maintainer
CBN2Path 1.2.0
CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunc...
3 versions - Latest release: 3 months ago - 2.7 thousand downloads total - 0 stars on GitHub - 2 maintainers
syntenet 1.14.0
Inference And Analysis Of Synteny Networks
11 versions - Latest release: 3 months ago - 1 dependent package - 14 thousand downloads total - 43 stars on GitHub - 1 maintainer
COSNet 1.46.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
7 versions - Latest release: 3 months ago - 24.2 thousand downloads total - 1 stars on GitHub
poem 1.4.0
POpulation-based Evaluation Metrics
4 versions - Latest release: 3 months ago - 4.51 thousand downloads total - 11 stars on GitHub - 1 maintainer
TMSig 1.6.0
Tools for Molecular Signatures
4 versions - Latest release: 3 months ago - 5.28 thousand downloads total - 4 stars on GitHub - 1 maintainer
KEGGlincs 1.38.0
Visualize all edges within a KEGG pathway and overlay LINCS data
7 versions - Latest release: 2 months ago - 21.4 thousand downloads total - 2 maintainers
jvecfor 1.0.0
Fast K-Nearest Neighbor Search for Single-Cell Analysis
1 version - Latest release: 4 months ago - 961 downloads total - 1 stars on GitHub - 1 maintainer
nethet 1.44.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
7 versions - Latest release: 3 months ago - 24.2 thousand downloads total - 2 maintainers
BatchQC 2.8.0
Batch Effects Quality Control Software
8 versions - Latest release: 3 months ago - 33.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.90.0
graph: A package to handle graph data structures
9 versions - Latest release: 4 months ago - 101 dependent packages - 3.72 million downloads total - 1 maintainer
PIUMA 1.8.0
Phenotypes Identification Using Mapper from topological data Analysis
6 versions - Latest release: 3 months ago - 6.76 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.74.0
Gene set enrichment data structures and methods
8 versions - Latest release: 4 months ago - 49 dependent packages - 1.5 million downloads total - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.72.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
7 versions - Latest release: 3 months ago - 13 dependent packages - 817 thousand downloads total - 1 maintainer
splineTimeR 1.40.0
Time-course differential gene expression data analysis using spline regression models followed by...
7 versions - Latest release: 3 months ago - 23 thousand downloads total - 2 maintainers
ternarynet 1.56.0
Ternary Network Estimation
7 versions - Latest release: 3 months ago - 28.9 thousand downloads total - 1 maintainer
CIMICE 1.20.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
7 versions - Latest release: 3 months ago - 11 thousand downloads total - 0 stars on GitHub - 1 maintainer
paircompviz 1.50.0
Multiple comparison test visualization
7 versions - Latest release: 3 months ago - 27.2 thousand downloads total - 1 maintainer
ibh 1.60.0
Interaction Based Homogeneity for Evaluating Gene Lists
7 versions - Latest release: 3 months ago - 32 thousand downloads total - 1 maintainer
csdR 1.18.0
Differential gene co-expression
7 versions - Latest release: 3 months ago - 9.83 thousand downloads total - 6 stars on GitHub - 1 maintainer
FELLA 1.32.0
Interpretation and enrichment for metabolomics data
7 versions - Latest release: 3 months ago - 27.5 thousand downloads total - 1 maintainer
GSEABenchmarkeR 1.32.0
Reproducible GSEA Benchmarking
8 versions - Latest release: 3 months ago - 2 dependent packages - 21.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
GmicR 1.26.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...
7 versions - Latest release: 3 months ago - 14.4 thousand downloads total - 1 maintainer
IMMAN 1.32.0
Interlog protein network reconstruction by Mapping and Mining ANalysis
7 versions - Latest release: 3 months ago - 16.3 thousand downloads total - 1 maintainer
gsean 1.32.0
Gene Set Enrichment Analysis with Networks
7 versions - Latest release: 3 months ago - 17.9 thousand downloads total - 1 maintainer
Pedixplorer 1.8.0
Pedigree Functions
5 versions - Latest release: 3 months ago - 7.63 thousand downloads total - 0 stars on GitHub - 1 maintainer
dcanr 1.28.0
Differential co-expression/association network analysis
7 versions - Latest release: 3 months ago - 1 dependent package - 22.2 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses
8 versions - Latest release: 3 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
BioNet 1.72.0
Routines for the functional analysis of biological networks
7 versions - Latest release: 3 months ago - 3 dependent packages - 90.4 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
rsbml 2.70.0
R support for SBML, using libsbml
7 versions - Latest release: 3 months ago - 3 dependent packages - 68 thousand downloads total - 1 maintainer
pandaR 1.44.0
PANDA Algorithm
7 versions - Latest release: 3 months ago - 1 dependent package - 28.8 thousand downloads total - 2 maintainers
MOSClip 1.6.0
Multi Omics Survival Clip
7 versions - Latest release: 3 months ago - 5.26 thousand downloads total - 1 stars on GitHub - 1 maintainer
netSmooth 1.32.0
Network smoothing for scRNAseq
7 versions - Latest release: 4 months ago - 1 dependent package - 19.1 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.52.0
a tool set for pathway based data integration and visualization
7 versions - Latest release: 3 months ago - 9 dependent packages - 733 thousand downloads total - 50 stars on GitHub - 1 maintainer
SBGNview 1.26.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
7 versions - Latest release: 4 months ago - 20.2 thousand downloads total - 29 stars on GitHub - 1 maintainer
airpart 1.20.0
Differential cell-type-specific allelic imbalance
7 versions - Latest release: 3 months ago - 14.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
sparsenetgls 1.30.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
7 versions - Latest release: 3 months ago - 13.4 thousand downloads total - 1 maintainer
tidyexposomics 1.0.0
Integrated Exposure-Omics Analysis Powered by Tidy Principles
1 version - Latest release: 4 months ago - 1.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
R3CPET 1.44.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
8 versions - Latest release: 3 months ago - 23.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
DeepPINCS 1.20.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
7 versions - Latest release: 3 months ago - 2 dependent packages - 11.6 thousand downloads total - 1 maintainer
fobitools 1.20.0
Tools for Manipulating the FOBI Ontology
7 versions - Latest release: 2 months ago - 11.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioNERO 1.20.0
Biological Network Reconstruction Omnibus
10 versions - Latest release: 4 months ago - 1 dependent package - 27.5 thousand downloads total - 32 stars on GitHub - 1 maintainer
TreeAndLeaf 1.24.0
Displaying binary trees with focus on dendrogram leaves
8 versions - Latest release: 3 months ago - 1 dependent package - 17.5 thousand downloads total - 1 maintainer
NetPathMiner 1.48.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
7 versions - Latest release: 4 months ago - 29.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.58.0
GRAPH Interaction from pathway Topological Environment
7 versions - Latest release: 3 months ago - 11 dependent packages - 447 thousand downloads total - 8 stars on GitHub - 1 maintainer
wppi 1.19.0
Weighting protein-protein interactions
8 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
hipathia 3.12.0
HiPathia: High-throughput Pathway Analysis
7 versions - Latest release: 4 months ago - 23.6 thousand downloads total - 1 maintainer
rTRM 1.50.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
7 versions - Latest release: 3 months ago - 1 dependent package - 33.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
DART 1.60.0
Denoising Algorithm based on Relevance network Topology
7 versions - Latest release: 3 months ago - 35.8 thousand downloads total - 1 maintainer
netZooR 1.16.0
A menagerie of methods for the inference and analysis of gene regulatory networks
8 versions - Latest release: 4 months ago - 7.64 thousand downloads total - 120 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
apComplex 2.78.0
Estimate protein complex membership using AP-MS protein data
7 versions - Latest release: 3 months ago - 56.9 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
hyperdraw 1.64.0
Visualizing Hypergaphs
7 versions - Latest release: 3 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.80.0
Render molecular pathways
7 versions - Latest release: 3 months ago - 42 thousand downloads total - 1 maintainer
netboost 2.20.0
Network Analysis Supported by Boosting
8 versions - Latest release: 3 months ago - 13 thousand downloads total - 1 maintainer
MetaboSignal 1.42.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
9 versions - Latest release: 20 days ago - 25.6 thousand downloads total - 2 maintainers
QuaternaryProd 1.46.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
7 versions - Latest release: 4 months ago - 21 thousand downloads total - 1 maintainer
CHRONOS 1.40.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
7 versions - Latest release: 3 months ago - 21.5 thousand downloads total - 1 maintainer
PANR 1.58.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...
7 versions - Latest release: 3 months ago - 32.4 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
qpgraph 2.46.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
7 versions - Latest release: 2 months ago - 1 dependent package - 76.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
GRaNIE 1.16.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...
7 versions - Latest release: 3 months ago - 13.1 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
SPIA 2.64.0
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation a...
7 versions - Latest release: 3 months ago - 3 dependent packages - 152 thousand downloads total - 1 maintainer
rScudo 1.28.0
Signature-based Clustering for Diagnostic Purposes
8 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.70.0
Mutual Information NETworks
7 versions - Latest release: 3 months ago - 9 dependent packages - 1 maintainer
RITAN 1.36.0
Rapid Integration of Term Annotation and Network resources
7 versions - Latest release: 3 months ago - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.60.0
Pathways from the NCI Pathways Database
7 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
pairkat 1.18.0
PaIRKAT
7 versions - Latest release: 3 months ago - 0 stars on GitHub - 1 maintainer
spatialHeatmap 2.18.2
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
18 versions - Latest release: 2 months ago - 4 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
goProfiles 1.74.0
goProfiles: an R package for the statistical analysis of functional profiles
7 versions - Latest release: 4 months ago - 1 dependent package - 55.9 thousand downloads total - 1 maintainer
scGraphVerse 1.2.0
scGraphVerse: A Gene Network Analysis Package
2 versions - Latest release: 3 months ago - 1.89 thousand downloads total - 1 stars on GitHub - 1 maintainer
spqn 1.24.0
Spatial quantile normalization
7 versions - Latest release: 3 months ago - 5 stars on GitHub - 1 maintainer
fgga 1.20.0
Hierarchical ensemble method based on factor graph
8 versions - Latest release: 3 months ago - 3 stars on GitHub - 1 maintainer
epiregulon.extra 1.8.0
Companion package to epiregulon with additional plotting, differential and graph functions
8 versions - Latest release: 3 months ago - 6.71 thousand downloads total - 0 stars on GitHub - 1 maintainer
DEsubs 1.38.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...
7 versions - Latest release: 3 months ago - 21.9 thousand downloads total - 2 maintainers
GRENITS 1.64.0
Gene Regulatory Network Inference Using Time Series
7 versions - Latest release: 3 months ago - 32.7 thousand downloads total - 1 maintainer
martini 1.32.0
GWAS Incorporating Networks
7 versions - Latest release: 3 months ago - 17.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
SGCP 1.11.1
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
10 versions - Latest release: 3 months ago - 8.47 thousand downloads total - 2 stars on GitHub - 1 maintainer
PathoStat 1.38.0
PathoStat Statistical Microbiome Analysis Package
7 versions - Latest release: 3 months ago - 22.2 thousand downloads total - 8 stars on GitHub - 2 maintainers
Top 9.7% on bioconductor.org
DEGraph 1.64.0
Two-sample tests on a graph
7 versions - Latest release: 3 months ago - 1 dependent package - 35.9 thousand downloads total - 1 maintainer
Related Keywords
Software 154 Network 91 GeneExpression 55 Pathways 48 Visualization 39 NetworkInference 38 SystemsBiology 33 Clustering 30 Microarray 29 NetworkEnrichment 28 GeneSetEnrichment 28 DifferentialExpression 26 RNASeq 26 KEGG 23 ImmunoOncology 21 Transcriptomics 17 GeneRegulation 17 Transcription 16 Sequencing 15 StatisticalMethod 14 Metabolomics 14 Regression 14 Classification 13 SingleCell 12 BiomedicalInformatics 11 Reactome 11 Genetics 10 Proteomics 10 GO 10 DimensionReduction 9 GeneTarget 9 ThirdPartyClient 9 Normalization 8 Bayesian 8 DataImport 8 Annotation 8 QualityControl 7 bioinformatics 7 CellBiology 6 r 6 mRNAMicroarray 6 DataRepresentation 6 MultipleComparison 6 GenePrediction 6 Preprocessing 5 GeneSignaling 5 Survival 5 FunctionalGenomics 5 PrincipalComponent 5 GeneticVariability 4 GenomeWideAssociation 4 GUI 4 r-package 4 ATACSeq 4 SNP 4 MassSpectrometry 3 DecisionTree 3 FeatureExtraction 3 TimeCourse 3 bioconductor 3 NeuralNetwork 3 Infrastructure 3 Epigenetics 3 TwoChannel 3 WorkflowStep 2 network-analysis 2 HiC 2 ChIPSeq 2 genomics 2 enrichment-analysis 2 Microbiome 2 Metagenomics 2 BatchEffect 2 CopyNumberVariation 2 networks 2 systems-biology 2 DNAMethylation 2 ReportWriting 2 DifferentialMethylation 2 SomaticMutation 2 Spatial 2 rstats 2 Phylogenetics 2 CellBasedAssays 2 network-science 2 pathways 2 DNASeq 2 gene-regulatory-network 2 MotifAnnotation 1 SequenceMatching 1 FunctionalPrediction 1 PatternLogic 1 TissueMicroarray 1 SupportVectorMachine 1 unsupervised-learning 1 ChipOnChip 1 semi-supervised-learning 1 self-training 1 networkclustering 1 graphs 1