Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "NetworkInference" keyword
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 36.3 thousand downloads total - 2 maintainers
GDCRNATools 1.22.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...3 versions - Latest release: 6 months ago - 36.3 thousand downloads total - 2 maintainers
SPONGE 1.24.0
Sparse Partial Correlations On Gene Expression3 versions - Latest release: 6 months ago - 2 dependent packages - 8.57 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
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
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
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression3 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 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
lpNet 2.34.2
Linear Programming Model for Network Inference4 versions - Latest release: 3 months ago - 19.1 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
SEPIRA 1.22.0 removed
Systems EPigenomics Inference of Regulatory Activity2 versions - Latest release: 6 months ago - 5.66 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
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
FRGEpistasis 1.38.0
Epistasis Analysis for Quantitative Traits by Functional Regression Model3 versions - Latest release: 6 months ago - 15.8 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
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
PrInCE 1.18.0
Predicting Interactomes from Co-Elution3 versions - Latest release: 6 months ago - 5.92 thousand downloads total - 6 stars on GitHub - 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
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
RegEnrich 1.12.1
Gene regulator enrichment analysis4 versions - Latest release: about 1 month ago - 4.65 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
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
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
TRONCO 2.34.0
TRONCO, an R package for TRanslational ONCOlogy3 versions - Latest release: 6 months ago - 16.6 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
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
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
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
CNORfeeder 1.42.0
Integration of CellNOptR to add missing links3 versions - Latest release: 6 months ago - 21.5 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
trena 1.24.0 removed
Fit transcriptional regulatory networks using gene expression, priors, machine learning2 versions - Latest release: 6 months ago - 7 thousand downloads total - 1 stars on GitHub - 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
netZooR 1.8.0
Unified methods for the inference and analysis of gene regulatory networks3 versions - Latest release: 9 days ago - 2.36 thousand downloads total - 84 stars on GitHub - 1 maintainer
netOmics 1.10.0
Multi-Omics (time-course) network-based integration and interpretation3 versions - Latest release: 9 days ago - 2.23 thousand downloads total - 5 stars on GitHub - 1 maintainer
epiregulon 1.0.0
Gene regulatory network inference from single cell epigenomic data1 version - Latest release: 22 days ago - 1 dependent package - 12 stars on GitHub - 1 maintainer
Informeasure 1.14.0
R implementation of information measures4 versions - Latest release: 11 days ago - 3.24 thousand downloads total - 2 stars on GitHub - 1 maintainer
netresponse 1.64.0
Functional Network Analysis3 versions - Latest release: 13 days ago - 25.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 14 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
GENIE3 1.26.0
GEne Network Inference with Ensemble of trees3 versions - Latest release: 14 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 14 days ago - 9 dependent packages - 122 thousand downloads total - 1 maintainer
minet 3.62.0
Mutual Information NETworks3 versions - Latest release: 14 days ago - 9 dependent packages - 122 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
4 versions - Latest release: 14 days ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
RedeR 3.0.0
Interactive visualization and manipulation of nested networks4 versions - Latest release: 14 days ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
fgga 1.12.0
Hierarchical ensemble method based on factor graph4 versions - Latest release: 14 days ago - 3.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network2 versions - Latest release: 14 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus5 versions - Latest release: 15 days ago - 1 dependent package - 8.17 thousand downloads total - 17 stars on GitHub - 1 maintainer
ceRNAnetsim 1.16.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)4 versions - Latest release: 16 days ago - 4.14 thousand downloads total - 4 stars on GitHub - 1 maintainer
CBNplot 1.4.0
plot bayesian network inferred from gene expression data based on enrichment analysis results4 versions - Latest release: 17 days ago - 2.56 thousand downloads total - 52 stars on GitHub - 1 maintainer
nempi 1.12.0
Inferring unobserved perturbations from gene expression data3 versions - Latest release: 21 days ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
mnem 1.20.0
Mixture Nested Effects Models3 versions - Latest release: 21 days ago - 4 dependent packages - 8.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
epiNEM 1.28.0
epiNEM3 versions - Latest release: 21 days ago - 4 dependent packages - 11.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
bnem 1.12.0
Training of logical models from indirect measurements of perturbation experiments3 versions - Latest release: 21 days ago - 3.03 thousand downloads total - 2 stars on GitHub - 1 maintainer
regutools 1.16.0
regutools: an R package for data extraction from RegulonDB3 versions - Latest release: 21 days ago - 4.33 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 21 days ago - 1 dependent package - 54.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
qpgraph 2.38.0
Estimation of genetic and molecular regulatory networks from high-throughput genomics data3 versions - Latest release: 21 days ago - 1 dependent package - 54.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
MIRit 0.99.13
Integrate microRNA and gene expression to decipher pathway complexity1 version - Latest release: 22 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
DeProViR 1.0.0
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...1 version - Latest release: 22 days ago - 165 downloads total - 1 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis2 versions - Latest release: 6 months ago - 8.52 thousand downloads total - 7 stars on GitHub - 1 maintainer
dcanr 1.18.0
Differential co-expression/association network analysis2 versions - Latest release: 6 months ago - 1 dependent package - 7.45 thousand downloads total - 5 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis2 versions - Latest release: 6 months ago - 4.35 thousand downloads total - 5 stars on GitHub - 1 maintainer
miRLAB 1.32.0
Dry lab for exploring miRNA-mRNA relationships2 versions - Latest release: 6 months ago - 13.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks2 versions - Latest release: 6 months ago - 1 dependent package - 9.31 thousand downloads total - 17 stars on GitHub - 1 maintainer
lionessR 1.16.0
Modeling networks for individual samples using LIONESS2 versions - Latest release: 6 months ago - 4.95 thousand downloads total - 20 stars on GitHub - 1 maintainer
multiSight 1.10.0
Multi-omics Classification, Functional Enrichment and Network Inference analysis2 versions - Latest release: 6 months ago - 2.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: 7 months ago - 3.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
66
Network
50
GeneExpression
38
GraphAndNetwork
36
SystemsBiology
27
GeneRegulation
20
Transcription
16
Pathways
14
NetworkEnrichment
12
GeneSetEnrichment
11
RNASeq
9
DifferentialExpression
9
Microarray
8
Transcriptomics
8
Bayesian
8
ImmunoOncology
7
Clustering
7
Regression
7
BiomedicalInformatics
6
Proteomics
6
Visualization
6
Classification
5
GenePrediction
5
KEGG
5
GeneTarget
5
SingleCell
5
TimeCourse
4
Genetics
4
FunctionalGenomics
4
Reactome
3
Survival
3
GeneticVariability
3
PrincipalComponent
3
ATACSeq
3
Normalization
3
StatisticalMethod
3
CellBiology
3
Sequencing
2
bioconductor
2
PooledScreens
2
FeatureExtraction
2
DimensionReduction
2
DecisionTree
2
NeuralNetwork
2
DNASeq
2
SomaticMutation
2
CRISPR
2
Preprocessing
2
miRNA
2
CellBasedAssays
2
Phylogenetics
2
Metabolomics
2
rstats
2
MassSpectrometry
2
GO
2
GUI
2
QualityControl
2
Epigenetics
1
SNP
1
regulondb
1
cdsb
1
AlternativeSplicing
1
tidygraph
1
GeneSignaling
1
DifferentialMethylation
1
tidyverse
1
Annotation
1
Coverage
1
visualization
1
network
1
bayesian
1
networks
1
systems-biology
1
biological-insights
1
biosigner
1
classification-models
1
multiplex-networks
1
computational-biology
1
complex-systems
1
deseq2
1
bioinformatics
1
multi-omics
1
MathematicalBiology
1
network-inference
1
BioCarta
1
omic
1
omic-datasets
1
omics
1
spls-da
1
StructuralPrediction
1
DataImport
1
TwoChannel
1
FunctionalPrediction
1
ChIPSeq
1
transcription-facto
1
dirichlet-process-mixtures
1
chromatin-interaction
1
chia-pet
1
HiC
1
synteny-network
1