Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "GraphAndNetwork" keyword
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 6 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
VennDetail 1.18.0
A package for visualization and extract details3 versions - Latest release: 6 months ago - 12 thousand downloads total - 24 stars on GitHub - 1 maintainer
hipathia 3.2.0
HiPathia: High-throughput Pathway Analysis3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 1 maintainer
syntenet 1.4.2
Inference And Analysis Of Synteny Networks4 versions - Latest release: about 1 month ago - 1 dependent package - 3.4 thousand downloads total - 14 stars on GitHub - 1 maintainer
spqn 1.14.0
Spatial quantile normalization3 versions - Latest release: 6 months ago - 4.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
2 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 1 maintainer
gaggle 1.70.0 removed
Broadcast data between R and Gaggle2 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 1 maintainer
PanViz 1.4.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data3 versions - Latest release: 6 months ago - 1.66 thousand downloads total - 3 stars on GitHub - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting3 versions - Latest release: 6 months ago - 4.72 thousand downloads total - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
BioNet 1.62.0
Routines for the functional analysis of biological networks3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects3 versions - Latest release: 6 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer
concordexR 1.2.0
Calculate the concordex coefficient3 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 6 stars on GitHub - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
R3CPET 1.34.1
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process4 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
RITAN 1.26.0
Rapid Integration of Term Annotation and Network resources3 versions - Latest release: 6 months ago - 9.59 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
RTN 2.26.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons3 versions - Latest release: 6 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
DART 1.50.0
Denoising Algorithm based on Relevance network Topology3 versions - Latest release: 6 months ago - 24 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 27.4 thousand downloads total - 1 maintainer
NCIgraph 1.50.0
Pathways from the NCI Pathways Database3 versions - Latest release: 6 months ago - 1 dependent package - 27.4 thousand downloads total - 1 maintainer
sparsenetgls 1.20.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...3 versions - Latest release: 6 months ago - 5.7 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.7 thousand downloads total - 1 maintainer
GraphAT 1.74.0
Graph Theoretic Association Tests3 versions - Latest release: 6 months ago - 29.7 thousand downloads total - 1 maintainer
GmicR 1.16.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...3 versions - Latest release: 6 months ago - 5.69 thousand downloads total - 1 maintainer
pareg 1.6.0
Pathway enrichment using a regularized regression approach3 versions - Latest release: 6 months ago - 1.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
diffuStats 1.22.0
Diffusion scores on biological networks3 versions - Latest release: 6 months ago - 9.33 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 41.2 thousand downloads total - 1 maintainer
apComplex 2.68.0
Estimate protein complex membership using AP-MS protein data3 versions - Latest release: 6 months ago - 41.2 thousand downloads total - 1 maintainer
COSNet 1.36.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings3 versions - Latest release: 6 months ago - 14.6 thousand downloads total - 1 stars on GitHub
ANF 1.24.1
Affinity Network Fusion for Complex Patient Clustering4 versions - Latest release: 3 months ago - 8.71 thousand downloads total - 1 maintainer
TreeAndLeaf 1.14.0
Displaying binary trees with focus on dendrogram leaves3 versions - Latest release: 6 months ago - 1 dependent package - 6.98 thousand downloads total - 1 maintainer
RCyjs 2.24.0
Display and manipulate graphs in cytoscape.js3 versions - Latest release: 6 months ago - 13.7 thousand downloads total - 1 maintainer
KBoost 1.10.0
Inference of gene regulatory networks from gene expression data3 versions - Latest release: 6 months ago - 2.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
CORREP 1.68.0
Multivariate Correlation Estimator and Statistical Inference Procedures.3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
IMMAN 1.22.0
Interlog protein network reconstruction by Mapping and Mining ANalysis3 versions - Latest release: 6 months ago - 7.17 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 39 thousand downloads total - 1 maintainer
keggorthology 2.54.0
graph support for KO, KEGG Orthology3 versions - Latest release: 6 months ago - 1 dependent package - 39 thousand downloads total - 1 maintainer
HGC 1.10.0
A fast hierarchical graph-based clustering method3 versions - Latest release: 6 months ago - 3.61 thousand downloads total - 1 maintainer
NeighborNet 1.20.0
Neighbor_net analysis3 versions - Latest release: 6 months ago - 4.32 thousand downloads total - 1 maintainer
enrichTF 1.18.0
Transcription Factors Enrichment Analysis3 versions - Latest release: 6 months ago - 6.82 thousand downloads total - 2 stars on GitHub - 1 maintainer
QuaternaryProd 1.36.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs3 versions - Latest release: 6 months ago - 12.3 thousand downloads total - 1 maintainer
EGAD 1.30.0
Extending guilt by association by degree3 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
DEsubs 1.28.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 maintainers
DeepPINCS 1.10.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning3 versions - Latest release: 6 months ago - 2 dependent packages - 3.51 thousand downloads total - 1 maintainer
netbiov 1.36.0 removed
A package for visualizing complex biological network2 versions - Latest release: 6 months ago - 15.8 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.7 thousand downloads total - 1 maintainer
SBMLR 1.98.0
SBML-R Interface and Analysis Tools3 versions - Latest release: 6 months ago - 29.7 thousand downloads total - 1 maintainer
Pigengene 1.28.0
Infers biological signatures from gene expression data3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
BiGGR 1.38.0
Constraint based modeling in R using metabolic reconstruction databases3 versions - Latest release: 6 months ago - 25.6 thousand downloads total - 2 maintainers
GRaNIE 1.6.1
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...3 versions - Latest release: 6 months ago - 3.75 thousand downloads total - 1 maintainer
Top 9.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 27 thousand downloads total - 1 maintainer
DEGraph 1.54.0
Two-sample tests on a graph3 versions - Latest release: 6 months ago - 1 dependent package - 27 thousand downloads total - 1 maintainer
CEMiTool 1.26.1
Co-expression Modules identification Tool4 versions - Latest release: about 1 month ago - 28.3 thousand downloads total - 1 maintainer
GeneNetworkBuilder 1.44.0
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-s...3 versions - Latest release: 6 months ago - 23.9 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goProfiles 1.64.0
goProfiles: an R package for the statistical analysis of functional profiles3 versions - Latest release: 6 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goSorensen 1.4.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)3 versions - Latest release: 6 months ago - 1.75 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
GraphAlignment 1.66.0
GraphAlignment3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 6 months ago - 7.94 thousand downloads total - 1 maintainer
GRENITS 1.54.0
Gene Regulatory Network Inference Using Time Series3 versions - Latest release: 6 months ago - 23.6 thousand downloads total - 1 maintainer
CausalR 1.34.0
Causal network analysis methods3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 2 maintainers
CoRegNet 1.40.0
CoRegNet : reconstruction and integrated analysis of co-regulatory networks3 versions - Latest release: 6 months ago - 16.9 thousand downloads total - 1 maintainer
PathoStat 1.28.0
PathoStat Statistical Microbiome Analysis Package3 versions - Latest release: 6 months ago - 11.4 thousand downloads total - 8 stars on GitHub - 2 maintainers
ternarynet 1.46.0
Ternary Network Estimation3 versions - Latest release: 6 months ago - 19.4 thousand downloads total - 1 maintainer
MetaboSignal 1.32.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways3 versions - Latest release: 5 months ago - 13.6 thousand downloads total - 2 maintainers
paircompviz 1.40.0
Multiple comparison test visualization3 versions - Latest release: 6 months ago - 17.5 thousand downloads total - 1 maintainer
csdR 1.8.0
Differential gene co-expression3 versions - Latest release: 6 months ago - 2.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 31.6 thousand downloads total - 1 maintainer
hyperdraw 1.54.0
Visualizing Hypergaphs3 versions - Latest release: 6 months ago - 1 dependent package - 31.6 thousand downloads total - 1 maintainer
pandaR 1.34.0
PANDA Algorithm3 versions - Latest release: 6 months ago - 1 dependent package - 16.7 thousand downloads total - 2 maintainers
Top 8.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 30 thousand downloads total - 1 maintainer
pathRender 1.70.0
Render molecular pathways3 versions - Latest release: 6 months ago - 30 thousand downloads total - 1 maintainer
TRONCO 2.34.0
TRONCO, an R package for TRanslational ONCOlogy3 versions - Latest release: 6 months ago - 16.6 thousand downloads total - 1 maintainer
sincell 1.34.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data3 versions - Latest release: 6 months ago - 15.2 thousand downloads total - 1 maintainer
Pi 2.14.0
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level3 versions - Latest release: 6 months ago - 17.9 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
ibh 1.50.0
Interaction Based Homogeneity for Evaluating Gene Lists3 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 1 maintainer
nethet 1.34.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity3 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 2 maintainers
RGraph2js 1.30.0
Convert a Graph into a D3js Script3 versions - Latest release: 6 months ago - 10.2 thousand downloads total - 1 maintainer
RTNsurvival 1.26.0
Survival analysis using transcriptional networks inferred by the RTN package3 versions - Latest release: 6 months ago - 8.93 thousand downloads total - 2 maintainers
RTNduals 1.26.0
Analysis of co-regulation and inference of 'dual regulons'3 versions - Latest release: 6 months ago - 1 dependent package - 10.1 thousand downloads total - 2 maintainers
Top 10.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 33.6 thousand downloads total - 1 maintainer
BioMVCClass 1.70.0
Model-View-Controller (MVC) Classes That Use Biobase3 versions - Latest release: 6 months ago - 33.6 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 30.5 thousand downloads total - 1 maintainer
MVCClass 1.76.0
Model-View-Controller (MVC) Classes3 versions - Latest release: 6 months ago - 1 dependent package - 30.5 thousand downloads total - 1 maintainer
wppi 1.10.0
Weighting protein-protein interactions3 versions - Latest release: 6 months ago - 3.14 thousand downloads total - 2 stars on GitHub - 1 maintainer
SQUADD 1.52.0
Add-on of the SQUAD Software3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 105 thousand downloads total - 1 maintainer
SPIA 2.54.0
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation a...3 versions - Latest release: 6 months ago - 3 dependent packages - 105 thousand downloads total - 1 maintainer
Top 6.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 50.8 thousand downloads total - 1 maintainer
biocGraph 1.64.0
Graph examples and use cases in Bioinformatics3 versions - Latest release: 6 months ago - 1 dependent package - 50.8 thousand downloads total - 1 maintainer
splineTimeR 1.30.0
Time-course differential gene expression data analysis using spline regression models followed by...3 versions - Latest release: 6 months ago - 12.4 thousand downloads total - 2 maintainers
CHRONOS 1.30.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis3 versions - Latest release: 6 months ago - 12 thousand downloads total - 1 maintainer
gsean 1.22.0
Gene Set Enrichment Analysis with Networks3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 1 maintainer
pairkat 1.8.0
PaIRKAT3 versions - Latest release: 6 months ago - 2.16 thousand downloads total - 0 stars on GitHub - 1 maintainer
PPInfer 1.28.0
Inferring functionally related proteins using protein interaction networks3 versions - Latest release: 6 months ago - 1 dependent package - 11.3 thousand downloads total - 1 maintainer
KEGGlincs 1.28.0
Visualize all edges within a KEGG pathway and overlay LINCS data3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 2 maintainers
PhenoGeneRanker 1.10.0
PhenoGeneRanker: A gene and phenotype prioritization tool3 versions - Latest release: 6 months ago - 2.65 thousand downloads total - 1 maintainer
airpart 1.10.0
Differential cell-type-specific allelic imbalance3 versions - Latest release: 6 months ago - 3.63 thousand downloads total - 2 stars on GitHub - 1 maintainer
FELLA 1.22.0
Interpretation and enrichment for metabolomics data3 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 1 maintainer
CIMICE 1.10.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution3 versions - Latest release: 6 months ago - 3.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
PANR 1.48.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...3 versions - Latest release: 6 months ago - 21.8 thousand downloads total - 1 maintainer
fcoex 1.16.0 removed
FCBF-based Co-Expression Networks for Single Cells2 versions - Latest release: 6 months ago - 5.4 thousand downloads total - 1 maintainer
BioNAR 1.4.4
Biological Network Analysis in R5 versions - Latest release: 2 months ago - 1.98 thousand downloads total - 1 maintainer
PIUMA 1.0.0
Phenotypes Identification Using Mapper from topological data Analysis1 version - Latest release: 21 days ago - 136 downloads total - 4 stars on GitHub - 1 maintainer
spatialHeatmap 2.10.0
spatialHeatmap8 versions - Latest release: 7 days ago - 5.78 thousand downloads total - 4 stars on GitHub - 1 maintainer
netSmooth 1.24.0
Network smoothing for scRNAseq3 versions - Latest release: 7 days ago - 1 dependent package - 8.4 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
3 versions - Latest release: 19 days ago - 33 dependent packages - 1.48 million downloads total - 1 maintainer
RBGL 1.80.0
An interface to the BOOST graph library3 versions - Latest release: 19 days ago - 33 dependent packages - 1.48 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
3 versions - Latest release: 19 days ago - 61 dependent packages - 1.52 million downloads total - 1 maintainer
Rgraphviz 2.48.0
Provides plotting capabilities for R graph objects3 versions - Latest release: 19 days ago - 61 dependent packages - 1.52 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
3 versions - Latest release: 19 days ago - 49 dependent packages - 976 thousand downloads total - 1 maintainer
GSEABase 1.66.0
Gene set enrichment data structures and methods3 versions - Latest release: 19 days ago - 49 dependent packages - 976 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
3 versions - Latest release: 19 days ago - 101 dependent packages - 2.56 million downloads total - 1 maintainer
graph 1.82.0
graph: A package to handle graph data structures3 versions - Latest release: 19 days ago - 101 dependent packages - 2.56 million downloads total - 1 maintainer
netZooR 1.8.0
Unified methods for the inference and analysis of gene regulatory networks3 versions - Latest release: 8 days ago - 2.36 thousand downloads total - 84 stars on GitHub - 1 maintainer
SBGNview 1.18.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"3 versions - Latest release: 8 days ago - 7.83 thousand downloads total - 23 stars on GitHub - 1 maintainer
Related Keywords
Software
144
Network
89
GeneExpression
53
Pathways
43
NetworkInference
36
Visualization
33
SystemsBiology
32
Microarray
29
Clustering
27
NetworkEnrichment
27
GeneSetEnrichment
26
DifferentialExpression
25
RNASeq
24
KEGG
22
ImmunoOncology
21
GeneRegulation
16
Transcriptomics
16
Transcription
16
Metabolomics
14
Sequencing
14
Regression
12
Classification
12
StatisticalMethod
11
BiomedicalInformatics
11
GO
10
SingleCell
10
Reactome
9
Proteomics
9
ThirdPartyClient
9
Genetics
9
GeneTarget
9
DataImport
8
Annotation
8
Normalization
8
bioinformatics
7
Bayesian
7
DimensionReduction
7
GenePrediction
6
QualityControl
6
mRNAMicroarray
6
CellBiology
6
Preprocessing
5
GeneSignaling
5
r
5
DataRepresentation
5
FunctionalGenomics
5
PrincipalComponent
5
MultipleComparison
5
Infrastructure
4
GenomeWideAssociation
4
GUI
4
GeneticVariability
4
Survival
4
SNP
4
NeuralNetwork
3
r-package
3
TimeCourse
3
MassSpectrometry
3
DecisionTree
3
ATACSeq
3
FeatureExtraction
3
bioconductor
3
TwoChannel
3
genomics
2
rstats
2
networks
2
network-science
2
gene-regulatory-network
2
ChIPSeq
2
Epigenetics
2
systems-biology
2
pathways
2
network-analysis
2
BatchEffect
2
DNASeq
2
SomaticMutation
2
ReportWriting
2
Phylogenetics
2
DNAMethylation
2
CellBasedAssays
2
CopyNumberVariation
2
enrichment-analysis
2
HiC
2
network-motifs
1
motif-analysis
1
cerna
1
mirna
1
network-biology
1
network-simulator
1
tcga
1
plotting
1
MotifDiscovery
1
snps
1
gwas
1
cran
1
core-services
1
SupportVectorMachine
1
text-mining
1
ggplot2
1
ontology
1