Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Network" 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
cliqueMS 1.16.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data3 versions - Latest release: 6 months ago - 7.77 thousand downloads total - 1 maintainer
MODA 1.28.0
MODA: MOdule Differential Analysis for weighted gene co-expression network3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
RLassoCox 1.10.0
A reweighted Lasso-Cox by integrating gene interaction information3 versions - Latest release: 6 months ago - 3.15 thousand downloads total - 3 stars on GitHub - 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
Linnorm 2.26.0
Linear model and normality based normalization and transformation method (Linnorm)3 versions - Latest release: 6 months ago - 1 dependent package - 22.4 thousand downloads total - 1 maintainer
SPEM 1.42.0
S-system parameter estimation method3 versions - Latest release: 6 months ago - 1 dependent package - 19.8 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
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
Top 7.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 38 thousand downloads total - 1 maintainer
ELMER 2.26.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes3 versions - Latest release: 6 months ago - 38 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
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
CeTF 1.14.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...3 versions - Latest release: 6 months ago - 6.04 thousand downloads total - 1 maintainer
SEPIRA 1.22.0 removed
Systems EPigenomics Inference of Regulatory Activity2 versions - Latest release: 6 months ago - 5.66 thousand downloads total - 1 maintainer
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
Path2PPI 1.32.0
Prediction of pathway-related protein-protein interaction networks3 versions - Latest release: 6 months ago - 12.6 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
DriverNet 1.42.0
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer3 versions - Latest release: 6 months ago - 21.3 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
Moonlight2R 1.2.0
Identify oncogenes and tumor suppressor genes from omics data2 versions - Latest release: 20 days ago - 1.06 thousand downloads total - 4 stars on GitHub - 1 maintainer
netprioR 1.28.0
A model for network-based prioritisation of genes3 versions - Latest release: 6 months ago - 9.03 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 6.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 40.4 thousand downloads total - 1 maintainer
pathifier 1.40.0
Quantify deregulation of pathways in cancer3 versions - Latest release: 6 months ago - 40.4 thousand downloads total - 1 maintainer
levi 1.20.0
Landscape Expression Visualization Interface3 versions - Latest release: 6 months ago - 5.47 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
Top 6.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 39.9 thousand downloads total - 1 maintainer
interactiveDisplay 1.40.0
Package for enabling powerful shiny web displays of Bioconductor objects3 versions - Latest release: 6 months ago - 1 dependent package - 39.9 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
mosbi 1.8.0
Molecular Signature identification using Biclustering3 versions - Latest release: 6 months ago - 2.63 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
netDx 1.14.0
Network-based patient classifier3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
FGNet 3.36.0
Functional Gene Networks derived from biological enrichment analyses3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
SANTA 2.38.0
Spatial Analysis of Network Associations3 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 0 stars on GitHub - 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
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 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
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 6 dependent packages - 37.4 thousand downloads total - 1 maintainer
CellNOptR 1.48.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...3 versions - Latest release: 6 months ago - 6 dependent packages - 37.4 thousand downloads total - 1 maintainer
BiRewire 3.34.0
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), u...3 versions - Latest release: 6 months ago - 26.2 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
LiquidAssociation 1.56.0
LiquidAssociation3 versions - Latest release: 6 months ago - 1 dependent package - 27.1 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
MethylMix 2.32.0
MethylMix: Identifying methylation driven cancer genes3 versions - Latest release: 6 months ago - 22.2 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
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
ADImpute 1.12.0
Adaptive Dropout Imputer (ADImpute)3 versions - Latest release: 6 months ago - 5.25 thousand downloads total - 0 stars on GitHub - 1 maintainer
RegEnrich 1.12.1
Gene regulator enrichment analysis4 versions - Latest release: about 1 month ago - 4.65 thousand downloads total - 1 maintainer
PathNet 1.42.0
An R package for pathway analysis using topological information3 versions - Latest release: 6 months ago - 20.3 thousand downloads total - 1 maintainer
transomics2cytoscape 1.12.0
A tool set for 3D Trans-Omic network visualization with Cytoscape3 versions - Latest release: 6 months ago - 3.65 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
fedup 1.10.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways3 versions - Latest release: 6 months ago - 2.96 thousand downloads total - 7 stars on GitHub - 1 maintainer
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
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
BayesKnockdown 1.28.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data3 versions - Latest release: 6 months ago - 9.92 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
vtpnet 0.42.0
variant-transcription factor-phenotype networks3 versions - Latest release: 6 months ago - 17.5 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
DeMAND 1.32.0
DeMAND3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 2 maintainers
XINA 1.20.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis3 versions - Latest release: 6 months ago - 6.4 thousand downloads total - 1 maintainer
MetID 1.20.0
Network-based prioritization of putative metabolite IDs3 versions - Latest release: 6 months ago - 5.66 thousand downloads total - 1 stars on GitHub - 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
RGMQL 1.22.1
GenoMetric Query Language for R/Bioconductor4 versions - Latest release: about 1 month ago - 6.14 thousand downloads total - 1 maintainer
AMOUNTAIN 1.28.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
SMITE 1.30.0
Significance-based Modules Integrating the Transcriptome and Epigenome3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 1 stars on GitHub - 2 maintainers
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
StarBioTrek 1.28.0
StarBioTrek3 versions - Latest release: 6 months ago - 10 thousand downloads total - 0 stars on GitHub - 1 maintainer
RGraph2js 1.30.0
Convert a Graph into a D3js Script3 versions - Latest release: 6 months ago - 10.2 thousand downloads total - 1 maintainer
mbOmic 1.6.0 removed
Integrative analysis of the microbiome and metabolome2 versions - Latest release: 6 months ago - 896 downloads total - 0 stars on GitHub - 1 maintainer
SingleCellSignalR 1.14.0
Cell Signalling Using Single Cell RNAseq Data Analysis3 versions - Latest release: 6 months ago - 3 dependent packages - 12 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
GNET2 1.18.0
Constructing gene regulatory networks from expression data through functional module inference3 versions - Latest release: 6 months ago - 5.66 thousand downloads total - 2 stars on GitHub - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
CNORfuzzy 1.44.0
Addon to CellNOptR: Fuzzy Logic3 versions - Latest release: 6 months ago - 21.3 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
KinSwingR 1.20.0
KinSwingR: network-based kinase activity prediction3 versions - Latest release: 6 months ago - 6.07 thousand downloads total - 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
HPiP 1.8.0
Host-Pathogen Interaction Prediction3 versions - Latest release: 6 months ago - 2.55 thousand downloads total - 3 stars on GitHub - 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
RCX 1.6.0
R package implementing the Cytoscape Exchange (CX) format3 versions - Latest release: 6 months ago - 1 dependent package - 3.4 thousand downloads total - 8 stars on GitHub - 1 maintainer
PCAN 1.30.0
Phenotype Consensus ANalysis (PCAN)3 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.10.0
PhenoGeneRanker: A gene and phenotype prioritization tool3 versions - Latest release: 6 months ago - 2.65 thousand downloads total - 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
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
CARNIVAL 2.14.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...3 versions - Latest release: 6 days ago - 2 dependent packages - 8.96 thousand downloads total - 53 stars on GitHub - 1 maintainer
Related Keywords
Software
180
GraphAndNetwork
89
GeneExpression
78
Pathways
59
NetworkInference
50
SystemsBiology
44
NetworkEnrichment
42
DifferentialExpression
39
Clustering
29
GeneRegulation
27
GeneSetEnrichment
27
RNASeq
26
Visualization
26
Microarray
24
KEGG
22
ImmunoOncology
21
Transcriptomics
20
Transcription
20
Sequencing
18
StatisticalMethod
17
Classification
17
Proteomics
14
GeneTarget
14
Metabolomics
14
SingleCell
14
Regression
13
GO
12
BiomedicalInformatics
11
Reactome
11
DataImport
11
Bayesian
10
bioinformatics
10
FunctionalGenomics
10
Genetics
10
Normalization
9
DNAMethylation
8
DifferentialMethylation
8
CellBiology
8
DataRepresentation
8
r
7
QualityControl
7
DimensionReduction
7
Preprocessing
7
mRNAMicroarray
7
Annotation
7
GenePrediction
7
Survival
7
TimeCourse
6
GeneSignaling
6
bioconductor
6
ThirdPartyClient
6
MethylationArray
6
GUI
6
GenomeWideAssociation
5
rstats
5
MultipleComparison
5
NeuralNetwork
5
Coverage
4
DNASeq
4
Infrastructure
4
SNP
4
FunctionalPrediction
4
pathways
4
TwoChannel
4
ATACSeq
4
miRNA
4
r-package
4
PrincipalComponent
3
CopyNumberVariation
3
FeatureExtraction
3
network
3
CellBasedAssays
3
comparative-genomics
3
DecisionTree
3
BatchEffect
3
ComparativeGenomics
3
Epigenetics
3
GeneticVariability
3
Phylogenetics
3
genomics
2
transcriptomics
2
SomaticMutation
2
BiologicalQuestion
2
systems-biology
2
WorkflowStep
2
Microbiome
2
networks
2
VariantAnnotation
2
network-analysis
2
ReportWriting
2
tcga
2
CRISPR
2
PooledScreens
2
bioconductor-package
2
pathway-analysis
2
bioconductor-packages
2
ShinyApps
2
AnnotationData
2
SequenceMatching
2
ChIPSeq
2