bioconductor.org "NetworkInference" keyword
GRENITS 1.62.0
Gene Regulatory Network Inference Using Time Series6 versions - Latest release: 5 months ago - 31.1 thousand downloads total - 1 maintainer
lpNet 2.42.0
Linear Programming Model for Network Inference7 versions - Latest release: 5 months ago - 26.6 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
BayesKnockdown 1.36.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data6 versions - Latest release: 5 months ago - 18.7 thousand downloads total - 1 maintainer
BulkSignalR 1.2.2
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...6 versions - Latest release: about 1 month ago - 6.15 thousand downloads total - 1 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
Path2PPI 1.40.0
Prediction of pathway-related protein-protein interaction networks6 versions - Latest release: 5 months ago - 21 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
TRONCO 2.42.0
TRONCO, an R package for TRanslational ONCOlogy7 versions - Latest release: 5 months ago - 26.9 thousand downloads total - 1 maintainer
cliqueMS 1.24.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data7 versions - Latest release: 5 months ago - 14.9 thousand downloads total - 1 maintainer
MOMA 1.22.0
Multi Omic Master Regulator Analysis6 versions - Latest release: 5 months ago - 11.7 thousand downloads total - 5 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
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
GNET2 1.26.0
Constructing gene regulatory networks from expression data through functional module inference6 versions - Latest release: 5 months ago - 12.5 thousand downloads total - 2 stars on GitHub - 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
CBNplot 1.10.0
plot bayesian network inferred from gene expression data based on enrichment analysis results8 versions - Latest release: 5 months ago - 9.99 thousand downloads total - 56 stars on GitHub - 1 maintainer
RegEnrich 1.20.0
Gene regulator enrichment analysis8 versions - Latest release: 5 months ago - 15.7 thousand downloads total - 1 maintainer
SPEM 1.50.0
S-system parameter estimation method6 versions - Latest release: 5 months ago - 1 dependent package - 28.2 thousand downloads total - 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
Top 7.7% on bioconductor.org
6 versions - Latest release: 5 months ago - 48.5 thousand downloads total - 2 maintainers
GDCRNATools 1.30.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...6 versions - Latest release: 5 months ago - 48.5 thousand downloads total - 2 maintainers
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
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
regutools 1.22.0
regutools: an R package for data extraction from RegulonDB6 versions - Latest release: 5 months ago - 11.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
SingleCellSignalR 2.0.1
Cell Signalling Using Single-Cell RNA-seq or Proteomics Data6 versions - Latest release: 5 months ago - 3 dependent packages - 25.4 thousand downloads total - 0 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
epiNEM 1.34.0
epiNEM6 versions - Latest release: 5 months ago - 4 dependent packages - 20.5 thousand downloads total - 1 stars on GitHub - 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
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
epiregulon 2.0.2
Gene regulatory network inference from single cell epigenomic data6 versions - Latest release: 4 months ago - 1 dependent package - 5.96 thousand downloads total - 12 stars on GitHub - 1 maintainer
CNORfeeder 1.50.0
Integration of CellNOptR to add missing links6 versions - Latest release: 5 months ago - 30.3 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
bnem 1.18.0
Training of logical models from indirect measurements of perturbation experiments6 versions - Latest release: 5 months ago - 9.91 thousand downloads total - 2 stars on GitHub - 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
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
PrInCE 1.26.0
Predicting Interactomes from Co-Elution6 versions - Latest release: 5 months ago - 12.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
HPiP 1.16.1
Host-Pathogen Interaction Prediction8 versions - Latest release: 17 days ago - 8.46 thousand downloads total - 3 stars on GitHub - 1 maintainer
lionessR 1.24.0
Modeling networks for individual samples using LIONESS6 versions - Latest release: 5 months ago - 12.5 thousand downloads total - 24 stars on GitHub - 1 maintainer
miRLAB 1.40.0
Dry lab for exploring miRNA-mRNA relationships6 versions - Latest release: 5 months ago - 22.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
nempi 1.18.0
Inferring unobserved perturbations from gene expression data6 versions - Latest release: 4 months ago - 9.27 thousand downloads total - 2 stars on GitHub - 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
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
MIRit 1.6.2
Integrate microRNA and gene expression to decipher pathway complexity9 versions - Latest release: about 2 months ago - 6.57 thousand downloads total - 2 stars on GitHub - 1 maintainer
tigre 1.64.0
Transcription factor Inference through Gaussian process Reconstruction of Expression6 versions - Latest release: 5 months ago - 35.6 thousand downloads total - 0 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
Informeasure 1.20.0
R implementation of information measures7 versions - Latest release: 5 months ago - 8.92 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
6 versions - Latest release: 5 months ago - 1 dependent package - 71.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
qpgraph 2.44.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data6 versions - Latest release: 5 months ago - 1 dependent package - 71.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
netZooR 1.14.2
A Menagerie of Methods for the Inference and Analysis of Gene Regulatory Networks7 versions - Latest release: 24 days ago - 6.5 thousand downloads total - 113 stars on GitHub - 1 maintainer
SPONGE 1.32.0
Sparse Partial Correlations On Gene Expression7 versions - Latest release: 5 months ago - 2 dependent packages - 15.9 thousand downloads total - 1 maintainer
fgga 1.18.0
Hierarchical ensemble method based on factor graph7 versions - Latest release: 5 months ago - 9.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
BioNERO 1.18.0
Biological Network Reconstruction Omnibus9 versions - Latest release: 5 months ago - 1 dependent package - 24.7 thousand downloads total - 32 stars on GitHub - 1 maintainer
mnem 1.26.0
Mixture Nested Effects Models6 versions - Latest release: 4 months ago - 4 dependent packages - 16.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
PANR 1.56.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...6 versions - Latest release: 5 months ago - 29.6 thousand downloads total - 1 maintainer
FRGEpistasis 1.46.0
Epistasis Analysis for Quantitative Traits by Functional Regression Model6 versions - Latest release: 5 months ago - 21.9 thousand downloads total - 1 maintainer
RTNsurvival 1.34.1
Survival analysis using transcriptional networks inferred by the RTN package7 versions - Latest release: about 1 month ago - 16.2 thousand downloads total - 2 maintainers
trena 1.24.0 removed
Fit transcriptional regulatory networks using gene expression, priors, machine learning2 versions - Latest release: over 2 years ago - 7 thousand downloads total - 1 stars on GitHub - 1 maintainer
netOmics 1.12.0 removed
Multi-Omics (time-course) network-based integration and interpretation4 versions - Latest release: over 1 year ago - 2.76 thousand downloads total - 14 stars on GitHub - 1 maintainer
DeProViR 1.4.0 removed
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...4 versions - Latest release: 11 months ago - 1.83 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioNetStat 1.24.0 removed
Biological Network Analysis3 versions - Latest release: almost 2 years ago - 9.35 thousand downloads total - 7 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: over 2 years ago - 3.82 thousand downloads total - 3 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: over 1 year ago - 1 dependent package - 10.7 thousand downloads total - 22 stars on GitHub - 1 maintainer
CoRegNet 1.42.0 removed
CoRegNet : reconstruction and integrated analysis of co-regulatory networks3 versions - Latest release: almost 2 years ago - 17.4 thousand downloads total - 1 maintainer
multiSight 1.10.0 removed
Multi-omics Classification, Functional Enrichment and Network Inference analysis2 versions - Latest release: over 2 years ago - 2.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
SEPIRA 1.22.0 removed
Systems EPigenomics Inference of Regulatory Activity2 versions - Latest release: over 2 years ago - 5.66 thousand downloads total - 1 maintainer
Related Keywords
Software
69
Network
53
GeneExpression
38
GraphAndNetwork
37
SystemsBiology
27
GeneRegulation
21
Transcription
16
Pathways
15
NetworkEnrichment
13
GeneSetEnrichment
12
RNASeq
12
Transcriptomics
10
DifferentialExpression
9
Proteomics
8
Microarray
8
Bayesian
8
SingleCell
7
Clustering
7
Visualization
7
ImmunoOncology
7
Regression
7
KEGG
6
BiomedicalInformatics
6
GeneTarget
5
Classification
5
GenePrediction
5
Reactome
4
FunctionalGenomics
4
Genetics
4
TimeCourse
4
GeneticVariability
3
StatisticalMethod
3
Sequencing
3
CellBiology
3
PrincipalComponent
3
Normalization
3
Survival
3
ATACSeq
3
QualityControl
2
mirna
2
PooledScreens
2
CellBasedAssays
2
Preprocessing
2
GO
2
Phylogenetics
2
NeuralNetwork
2
SomaticMutation
2
MassSpectrometry
2
Metabolomics
2
DimensionReduction
2
DecisionTree
2
FeatureExtraction
2
bioconductor
2
GUI
2
miRNA
2
CRISPR
2
DNASeq
2
rstats
2
SNP
1
synteny-network
1
gene-regulatory-network
1
synteny
1
phylogenomics
1
network-science
1
evolutionary-genomics
1
comparative-genomics
1
WholeGenome
1
ComparativeGenomics
1
mirnaseq-analysis
1
mirna-seq
1
mirna-mrna-interaction
1
network-inference
1
multi-omics
1
omic
1
omic-datasets
1
omics
1
deseq2
1
classification-models
1
biosigner
1
biological-insights
1
systems-biology
1
spls-da
1
networks
1
multiplex-networks
1
computational-biology
1
complex-systems
1
bioinformatics
1
MathematicalBiology
1
BioCarta
1
Coverage
1
Annotation
1
AlternativeSplicing
1
WorkflowStep
1
SupportVectorMachine
1
RandomForest
1
MachineLearning
1
transcription-factors
1
Epigenetics
1
network-simulator
1
network-biology
1