Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "NetworkEnrichment" keyword
GSEABenchmarkeR 1.24.0
Reproducible GSEA Benchmarking3 versions - Latest release: about 1 month ago - 2 dependent packages - 9.59 thousand downloads total - 13 stars on GitHub - 1 maintainer
pathlinkR 1.0.0
Analyze and interpret RNA-Seq results1 version - Latest release: about 1 month ago - 446 downloads total - 4 stars on GitHub - 1 maintainer
MIRit 0.99.13
Integrate microRNA and gene expression to decipher pathway complexity2 versions - Latest release: about 1 month ago - 346 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 5 dependent packages - 50.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
EnrichmentBrowser 2.32.0
Seamless navigation through combined results of set-based and network-based enrichment analysis3 versions - Latest release: 7 months ago - 5 dependent packages - 50.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
Moonlight2R 1.2.0
Identify oncogenes and tumor suppressor genes from omics data2 versions - Latest release: about 1 month ago - 1.13 thousand downloads total - 4 stars on GitHub - 1 maintainer
GWENA 1.12.0
Pipeline for augmented co-expression analysis3 versions - Latest release: 6 months ago - 7.57 thousand downloads total - 18 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
SGCP 1.2.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...3 versions - Latest release: 7 months ago - 1.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
paxtoolsr 1.36.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons3 versions - Latest release: 6 months ago - 24 thousand downloads total - 10 stars on GitHub - 1 maintainer
BioCor 1.26.0
Functional similarities3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
diggit 1.34.0
Inference of Genetic Variants Driving Cellular Phenotypes3 versions - Latest release: 7 months ago - 13.4 thousand downloads total - 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
Top 6.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 7 dependent packages - 57.3 thousand downloads total - 1 maintainer
viper 1.36.0
Virtual Inference of Protein-activity by Enriched Regulon analysis3 versions - Latest release: 7 months ago - 7 dependent packages - 57.3 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 33.1 thousand downloads total - 1 maintainer
miRNApath 1.62.0
miRNApath: Pathway Enrichment for miRNA Expression Data3 versions - Latest release: 7 months ago - 33.1 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
3 versions - Latest release: 7 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: 7 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: 7 months ago - 3.73 thousand downloads total - 9 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
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
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
pareg 1.6.0
Pathway enrichment using a regularized regression approach3 versions - Latest release: 7 months ago - 1.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 7 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: 7 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
miRspongeR 2.6.0
Identification and analysis of miRNA sponge regulation3 versions - Latest release: 7 months ago - 1 dependent package - 6.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
SANTA 2.38.0
Spatial Analysis of Network Associations3 versions - Latest release: 7 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: 7 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: 7 months ago - 11.1 thousand downloads total - 2 maintainers
Top 9.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 27 thousand downloads total - 1 maintainer
DEGraph 1.54.0
Two-sample tests on a graph3 versions - Latest release: 7 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
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: 7 months ago - 20.3 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
fedup 1.10.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways3 versions - Latest release: 7 months ago - 2.96 thousand downloads total - 7 stars on GitHub - 1 maintainer
DeMAND 1.32.0
DeMAND3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 2 maintainers
SMITE 1.30.0
Significance-based Modules Integrating the Transcriptome and Epigenome3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 1 stars on GitHub - 2 maintainers
Top 9.8% on bioconductor.org
4 versions - Latest release: 5 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 5 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: 7 months ago - 21.9 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
signatureSearch 1.16.0
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis3 versions - Latest release: 7 months ago - 10.6 thousand downloads total - 17 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
gsean 1.22.0
Gene Set Enrichment Analysis with Networks3 versions - Latest release: 7 months ago - 7.81 thousand downloads total - 1 maintainer
PPInfer 1.28.0
Inferring functionally related proteins using protein interaction networks3 versions - Latest release: 7 months ago - 1 dependent package - 11.3 thousand downloads total - 1 maintainer
vulcan 1.24.0
VirtUaL ChIP-Seq data Analysis using Networks3 versions - Latest release: 7 months ago - 8.7 thousand downloads total - 1 maintainer
FELLA 1.22.0
Interpretation and enrichment for metabolomics data3 versions - Latest release: 7 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: 7 months ago - 5.4 thousand downloads total - 1 maintainer
MoonlightR 1.30.0
Identify oncogenes and tumor suppressor genes from omics data3 versions - Latest release: about 1 month ago - 11.7 thousand downloads total - 17 stars on GitHub - 1 maintainer
enrichViewNet 1.2.0
From functional enrichment results to biological networks2 versions - Latest release: 22 days ago - 930 downloads total - 5 stars on GitHub - 1 maintainer
omicsViewer 1.8.0
Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omics...3 versions - Latest release: 24 days ago - 2.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
4 versions - Latest release: 25 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: 25 days ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
vissE 1.12.0
Visualising Set Enrichment Analysis Results3 versions - Latest release: 25 days ago - 4.17 thousand downloads total - 10 stars on GitHub - 1 maintainer
magrene 1.6.0
Motif Analysis In Gene Regulatory Networks3 versions - Latest release: 26 days ago - 1.45 thousand downloads total - 1 stars on GitHub - 1 maintainer
cageminer 1.10.0
Candidate Gene Miner3 versions - Latest release: 26 days ago - 2.64 thousand downloads total - 1 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: 28 days ago - 2.56 thousand downloads total - 52 stars on GitHub - 1 maintainer
netboxr 1.11.0 removed
netboxr1 version - Latest release: 8 months ago - 2.92 thousand downloads total - 1 maintainer
Related Keywords
Software
53
Network
42
GeneExpression
31
GraphAndNetwork
27
GeneSetEnrichment
24
Pathways
23
DifferentialExpression
20
SystemsBiology
17
RNASeq
13
NetworkInference
12
KEGG
10
GeneRegulation
10
Visualization
9
ImmunoOncology
8
GO
8
Microarray
7
StatisticalMethod
6
Clustering
6
FunctionalGenomics
6
Survival
5
Transcriptomics
5
FunctionalPrediction
5
mRNAMicroarray
4
Sequencing
4
bioinformatics
4
Reactome
4
Regression
3
DataImport
3
GeneTarget
3
Transcription
3
network
3
DifferentialMethylation
3
Coverage
2
pathways
2
ReportWriting
2
Metabolomics
2
networks
2
r
2
Annotation
2
MultipleComparison
2
visualization
2
SingleCell
2
Classification
2
MotifDiscovery
2
bioconductor
2
TwoChannel
2
QualityControl
2
gene
2
mirna
2
BiomedicalInformatics
2
DNAMethylation
2
MethylationArray
2
DecisionTree
1
sponge
1
enrichment
1
GenePrediction
1
Normalization
1
graphs
1
bayesian
1
Bayesian
1
VariantAnnotation
1
SNP
1
GenomeWideAssociation
1
rstats
1
network-science
1
network-motifs
1
motif-analysis
1
gene-regulatory-network
1
GUI
1
r-package
1
functional-enrichment
1
cystocape
1
BiologicalQuestion
1
ChIPSeq
1
TimeCourse
1
Proteomics
1
OneChannel
1
Genetics
1
GeneSignaling
1
GenomeAnnotation
1
genecoexpressionnetwork
1
clustering
1
NeuralNetwork
1
DimensionReduction
1
FeatureExtraction
1
transcriptomics
1
pipeline
1
network-analysis
1
enrichment-analysis
1
co-expression
1
mirnaseq-analysis
1
mirna-seq
1
mirna-mrna-interaction
1
Epigenetics
1
pathway-enrichment-analysis
1
bioconductor-package
1
cerna
1
Spatial
1
Infrastructure
1
DataRepresentation
1