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
epiregulon 1.0.0
Gene regulatory network inference from single cell epigenomic data1 version - Latest release: about 1 month ago - 1 dependent package - 194 downloads total - 12 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: about 1 month ago - 364 downloads total - 1 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis3 versions - Latest release: 6 months ago - 8.68 thousand downloads total - 7 stars on GitHub - 1 maintainer
miRLAB 1.32.0
Dry lab for exploring miRNA-mRNA relationships3 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
dcanr 1.18.0
Differential co-expression/association network analysis3 versions - Latest release: 6 months ago - 1 dependent package - 7.93 thousand downloads total - 5 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis3 versions - Latest release: 6 months ago - 4.74 thousand downloads total - 5 stars on GitHub - 1 maintainer
lionessR 1.16.0
Modeling networks for individual samples using LIONESS3 versions - Latest release: 6 months ago - 5.33 thousand downloads total - 20 stars on GitHub - 1 maintainer
multiSight 1.10.0 removed
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
Top 7.7% on bioconductor.org
3 versions - Latest release: 7 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: 7 months ago - 36.3 thousand downloads total - 2 maintainers
SPONGE 1.24.0
Sparse Partial Correlations On Gene Expression3 versions - Latest release: 7 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: 7 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: 7 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: 7 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: 7 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: 7 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: 7 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: 7 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: 7 months ago - 5.66 thousand downloads total - 1 maintainer
Path2PPI 1.32.0
Prediction of pathway-related protein-protein interaction networks3 versions - Latest release: 7 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: 7 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: 7 months ago - 15.8 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 7 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: 7 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: 7 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: 7 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: 7 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: 7 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: 7 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: 7 months ago - 16.9 thousand downloads total - 1 maintainer
BayesKnockdown 1.28.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data3 versions - Latest release: 7 months ago - 9.92 thousand downloads total - 1 maintainer
pandaR 1.34.0
PANDA Algorithm3 versions - Latest release: 7 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: 7 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: 7 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: 7 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: 7 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: 7 months ago - 12.4 thousand downloads total - 2 maintainers
HPiP 1.8.0
Host-Pathogen Interaction Prediction3 versions - Latest release: 7 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: 7 months ago - 10.9 thousand downloads total - 2 maintainers
CNORfeeder 1.42.0
Integration of CellNOptR to add missing links3 versions - Latest release: 7 months ago - 21.5 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.10.0
PhenoGeneRanker: A gene and phenotype prioritization tool3 versions - Latest release: 7 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: 7 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: 7 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: 7 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: 19 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: 19 days ago - 2.23 thousand downloads total - 5 stars on GitHub - 1 maintainer
Informeasure 1.14.0
R implementation of information measures4 versions - Latest release: 21 days ago - 3.24 thousand downloads total - 2 stars on GitHub - 1 maintainer
netresponse 1.64.0
Functional Network Analysis3 versions - Latest release: 23 days ago - 25.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 23 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: 23 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 24 days ago - 9 dependent packages - 122 thousand downloads total - 1 maintainer
minet 3.62.0
Mutual Information NETworks3 versions - Latest release: 24 days ago - 9 dependent packages - 122 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
4 versions - Latest release: 24 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: 24 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: 24 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: 24 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus5 versions - Latest release: 25 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: 25 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: 27 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: about 1 month ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
mnem 1.20.0
Mixture Nested Effects Models3 versions - Latest release: about 1 month ago - 4 dependent packages - 8.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
epiNEM 1.28.0
epiNEM3 versions - Latest release: about 1 month 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: about 1 month 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: about 1 month ago - 4.33 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: about 1 month 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: about 1 month 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: about 1 month ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: 8 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
DifferentialExpression
9
RNASeq
9
Transcriptomics
8
Microarray
8
Bayesian
8
Clustering
7
ImmunoOncology
7
Regression
7
BiomedicalInformatics
6
Visualization
6
Proteomics
6
GeneTarget
5
GenePrediction
5
KEGG
5
Classification
5
SingleCell
5
TimeCourse
4
FunctionalGenomics
4
Genetics
4
Normalization
3
Survival
3
GeneticVariability
3
PrincipalComponent
3
ATACSeq
3
StatisticalMethod
3
Reactome
3
CellBiology
3
GO
2
PooledScreens
2
DNASeq
2
CRISPR
2
MassSpectrometry
2
Phylogenetics
2
rstats
2
Preprocessing
2
CellBasedAssays
2
QualityControl
2
DimensionReduction
2
DecisionTree
2
GUI
2
miRNA
2
bioconductor
2
SomaticMutation
2
FeatureExtraction
2
NeuralNetwork
2
Metabolomics
2
Sequencing
2
cerna
1
r-package
1
cran
1
core-services
1
mRNAMicroarray
1
DNAMethylation
1
SupportVectorMachine
1
WorkflowStep
1
transcription-factors
1
gene-regulatory-network
1
Technology
1
ResearchField
1
BiologicalQuestion
1
BioCarta
1
ThirdPartyClient
1
Coverage
1
Annotation
1
AlternativeSplicing
1
Epigenetics
1
SNP
1
regulondb
1
cdsb
1
GeneSignaling
1
DifferentialMethylation
1
visualization
1
network
1
bayesian
1
tidyverse
1
tidygraph
1
tcga
1
r
1
network-simulator
1
network-biology
1
mirna
1
biosigner
1
classification-models
1
synteny-network
1
synteny
1
deseq2
1
phylogenomics
1
network-science
1
evolutionary-genomics
1
comparative-genomics
1