Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "GeneSetEnrichment" keyword
mosdef 1.0.0
MOSt frequently used and useful Differential Expression Functions1 version - Latest release: about 1 month ago - 0 stars on GitHub - 1 maintainer
sparrow 1.10.0
Take command of set enrichment analyses through a unified interface4 versions - Latest release: about 1 month ago - 1 dependent package - 4.36 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
3 versions - Latest release: 30 days ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
enrichplot 1.24.0
Visualization of Functional Enrichment Result3 versions - Latest release: 30 days ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
3 versions - Latest release: 30 days ago - 49 dependent packages - 983 thousand downloads total - 1 maintainer
GSEABase 1.66.0
Gene set enrichment data structures and methods3 versions - Latest release: 30 days ago - 49 dependent packages - 983 thousand downloads total - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis3 versions - Latest release: 7 months ago - 17.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
iSEEpathways 1.0.0
iSEE extension for panels related to pathway analysis2 versions - Latest release: 7 months ago - 1.03 thousand downloads total - 1 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
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...3 versions - Latest release: 27 days ago - 1.3 thousand downloads total - 9 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
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 23 dependent packages - 504 thousand downloads total - 1 maintainer
GOstats 2.68.0
Tools for manipulating GO and microarrays3 versions - Latest release: 7 months ago - 23 dependent packages - 504 thousand downloads total - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations3 versions - Latest release: 6 months ago - 1 dependent package - 24.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
ctsGE 1.28.0
Clustering of Time Series Gene Expression data3 versions - Latest release: 6 months ago - 11.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioQC 1.30.0
Detect tissue heterogeneity in expression profiles with gene sets3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
3 versions - Latest release: 7 months ago - 15 dependent packages - 443 thousand downloads total - 1 maintainer
ReactomePA 1.46.0
Reactome Pathway Analysis3 versions - Latest release: 7 months ago - 15 dependent packages - 443 thousand downloads total - 1 maintainer
famat 1.12.0
Functional analysis of metabolic and transcriptomic data3 versions - Latest release: 6 months ago - 3.63 thousand 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
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
fenr 1.0.5
Fast functional enrichment for interactive applications5 versions - Latest release: 3 months ago - 1.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
3 versions - Latest release: 28 days ago - 38 dependent packages - 1.17 million downloads total - 345 stars on GitHub - 1 maintainer
fgsea 1.30.0
Fast Gene Set Enrichment Analysis3 versions - Latest release: 28 days ago - 38 dependent packages - 1.17 million downloads total - 345 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 38 stars on GitHub - 1 maintainer
singscore 1.22.0
Rank-based single-sample gene set scoring method3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 38 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
3 versions - Latest release: 7 months ago - 13 dependent packages - 515 thousand downloads total - 1 maintainer
Category 2.68.0
Category Analysis3 versions - Latest release: 7 months ago - 13 dependent packages - 515 thousand downloads total - 1 maintainer
simplifyEnrichment 1.12.0
Simplify Functional Enrichment Results3 versions - Latest release: 6 months ago - 4 dependent packages - 23.2 thousand downloads total - 96 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
transcriptogramer 1.24.0
Transcriptional analysis based on transcriptograms3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 4 stars on GitHub - 1 maintainer
loci2path 1.22.0
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs3 versions - Latest release: 6 months ago - 7.21 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
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
NoRCE 1.14.0
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment3 versions - Latest release: 6 months ago - 4.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 6 dependent packages - 161 thousand downloads total - 218 stars on GitHub - 1 maintainer
MAST 1.28.0
Model-based Analysis of Single Cell Transcriptomics3 versions - Latest release: 6 months ago - 6 dependent packages - 161 thousand downloads total - 218 stars on GitHub - 1 maintainer
methylGSA 1.20.0
Gene Set Analysis Using the Outcome of Differential Methylation3 versions - Latest release: 7 months ago - 11.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 25 days ago - 3.18 thousand downloads total - 3 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
RGSEA 1.36.0
Random Gene Set Enrichment Analysis3 versions - Latest release: 7 months ago - 17.3 thousand downloads total - 1 maintainer
CelliD 1.10.1
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis4 versions - Latest release: 6 months ago - 9.32 thousand downloads total - 1 maintainer
npGSEA 1.38.0
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)3 versions - Latest release: 7 months ago - 17.7 thousand downloads total - 1 maintainer
cpvSNP 1.34.0
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets3 versions - Latest release: 7 months ago - 13.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry3 versions - Latest release: 7 months ago - 9.23 thousand downloads total - 1 maintainer
INTACT 1.2.0
Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis3 versions - Latest release: 7 months ago - 1.24 thousand downloads total - 8 stars on GitHub - 1 maintainer
SigCheck 2.34.0
Check a gene signature's prognostic performance against random signatures, known signatures, and ...3 versions - Latest release: 7 months ago - 14.4 thousand downloads total - 1 maintainer
chipenrich 2.26.0
Gene Set Enrichment For ChIP-seq Peak Data3 versions - Latest release: 7 months ago - 27.8 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 7 months ago - 4.36 thousand downloads total - 1 maintainer
HPAStainR 1.12.0 removed
Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes2 versions - Latest release: 7 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 7 months ago - 9.18 thousand downloads total - 1 maintainer
pathVar 1.32.0
Methods to Find Pathways with Significantly Different Variability3 versions - Latest release: 7 months ago - 9.78 thousand downloads total - 1 maintainer
nullranges 1.8.0
Generation of null ranges via bootstrapping or covariate matching3 versions - Latest release: 7 months ago - 1 dependent package - 4.44 thousand downloads total - 22 stars on GitHub - 1 maintainer
dcGSA 1.30.0
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles3 versions - Latest release: 7 months ago - 10.5 thousand downloads total - 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
GOfuncR 1.22.2
Gene ontology enrichment using FUNC4 versions - Latest release: 3 months ago - 20.3 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
Top 9.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
MAGeCKFlute 2.6.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens3 versions - Latest release: 7 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
GIGSEA 1.20.0
Genotype Imputed Gene Set Enrichment Analysis3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets3 versions - Latest release: 7 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
CAFE 1.38.0
Chromosmal Aberrations Finder in Expression data3 versions - Latest release: 7 months ago - 17.6 thousand downloads total - 1 maintainer
ttgsea 1.10.0
Tokenizing Text of Gene Set Enrichment Analysis3 versions - Latest release: 7 months ago - 2 dependent packages - 3.68 thousand downloads total - 1 maintainer
GSRI 2.50.0
Gene Set Regulation Index3 versions - Latest release: 7 months ago - 25.8 thousand downloads total - 1 maintainer
ADAMgui 1.18.0
Activity and Diversity Analysis Module Graphical User Interface3 versions - Latest release: 7 months ago - 6.89 thousand downloads total - 1 maintainer
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges3 versions - Latest release: 7 months ago - 5 dependent packages - 25 thousand downloads total - 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
GSALightning 1.30.0
Fast Permutation-based Gene Set Analysis3 versions - Latest release: 7 months ago - 10.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
SISPA 1.32.0 removed
SISPA: Method for Sample Integrated Set Profile Analysis2 versions - Latest release: 7 months ago - 13.4 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: 7 months ago - 7.55 thousand downloads total - 1 maintainer
coRdon 1.20.0
Codon Usage Analysis and Prediction of Gene Expressivity3 versions - Latest release: 7 months ago - 13 thousand downloads total - 17 stars on GitHub - 1 maintainer
gep2pep 1.22.0
Creation and Analysis of Pathway Expression Profiles (PEPs)3 versions - Latest release: 7 months ago - 7.44 thousand downloads total - 1 maintainer
LRcell 1.10.0
Differential cell type change analysis using Logistic/linear Regression3 versions - Latest release: 7 months ago - 3.04 thousand downloads total - 3 stars on GitHub - 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
canceR 1.36.8
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC6 versions - Latest release: about 1 month ago - 19 thousand downloads total - 8 stars on GitHub - 1 maintainer
KnowSeq 1.16.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline3 versions - Latest release: 7 months ago - 6.15 thousand downloads total - 1 maintainer
CBEA 1.3.0
Competitive Balances for Taxonomic Enrichment Analysis in R3 versions - Latest release: 8 months ago - 2.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goProfiles 1.64.0
goProfiles: an R package for the statistical analysis of functional profiles3 versions - Latest release: 7 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goSorensen 1.4.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)3 versions - Latest release: 7 months ago - 1.75 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
TissueEnrich 1.22.0
Tissue-specific gene enrichment analysis3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
transite 1.20.1
RNA-binding protein motif analysis4 versions - Latest release: 3 months ago - 6.54 thousand downloads total - 1 maintainer
PloGO2 1.14.0
Plot Gene Ontology and KEGG pathway Annotation and Abundance3 versions - Latest release: 7 months ago - 4.63 thousand downloads total - 2 maintainers
attract 1.54.0
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor La...3 versions - Latest release: 7 months ago - 29.9 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
PanomiR 1.6.0
Detection of miRNAs that regulate interacting groups of pathways3 versions - Latest release: 7 months ago - 2.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
ViSEAGO 1.16.0
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and seman...3 versions - Latest release: 7 months ago - 12 thousand downloads total - 1 maintainer
sincell 1.34.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data3 versions - Latest release: 7 months ago - 15.2 thousand downloads total - 1 maintainer
goSTAG 1.26.0
A tool to use GO Subtrees to Tag and Annotate Genes within a set3 versions - Latest release: 7 months ago - 9.53 thousand downloads total - 1 maintainer
oppar 1.30.0
Outlier profile and pathway analysis in R3 versions - Latest release: 7 months ago - 10.1 thousand downloads total - 1 maintainer
oposSOM 2.20.0
Comprehensive analysis of transcriptome data3 versions - Latest release: 7 months ago - 17.7 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 28.7 thousand downloads total - 1 maintainer
iBBiG 1.46.0
Iterative Binary Biclustering of Genesets3 versions - Latest release: 7 months ago - 1 dependent package - 28.7 thousand downloads total - 1 maintainer
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
eegc 1.28.0
Engineering Evaluation by Gene Categorization (eegc)3 versions - Latest release: 7 months ago - 9.92 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
gCrisprTools 2.8.0
Suite of Functions for Pooled Crispr Screen QC and Analysis3 versions - Latest release: 7 months ago - 11.6 thousand downloads total - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 7 months ago - 5.12 thousand downloads total - 1 maintainer
ADAM 1.18.0
ADAM: Activity and Diversity Analysis Module3 versions - Latest release: 7 months ago - 1 dependent package - 7.52 thousand downloads total - 1 maintainer
RCAS 1.28.3
RNA Centric Annotation System4 versions - Latest release: 3 months ago - 1 dependent package - 13.1 thousand downloads total - 1 maintainer
Related Keywords
Software
162
GeneExpression
96
Pathways
74
DifferentialExpression
63
RNASeq
57
Visualization
43
Microarray
41
ImmunoOncology
40
GO
39
Sequencing
36
Transcription
32
Clustering
30
Network
27
Transcriptomics
27
GraphAndNetwork
26
MultipleComparison
25
KEGG
25
SystemsBiology
25
NetworkEnrichment
24
Annotation
22
FunctionalGenomics
21
GeneRegulation
20
Regression
20
QualityControl
18
Genetics
18
BiomedicalInformatics
16
Normalization
16
Reactome
16
DataImport
14
Epigenetics
14
Proteomics
14
SingleCell
13
GeneTarget
13
Classification
13
Preprocessing
13
TimeCourse
11
NetworkInference
11
BatchEffect
11
StatisticalMethod
10
Bayesian
10
ReportWriting
9
r
9
bioconductor
9
Metabolomics
9
CellBiology
9
bioinformatics
9
AlternativeSplicing
9
ChIPSeq
9
mRNAMicroarray
8
Survival
8
OneChannel
7
DNAMethylation
7
DifferentialMethylation
7
DifferentialSplicing
7
shiny
6
DimensionReduction
6
GenomeAnnotation
6
GUI
6
TwoChannel
6
Coverage
6
ShinyApps
5
FunctionalPrediction
5
GeneticVariability
5
DataRepresentation
5
MethylationArray
5
GenePrediction
5
SNP
5
PrincipalComponent
5
ATACSeq
5
GenomeWideAssociation
5
bioconductor-package
4
GeneSignaling
4
transcriptomics
4
enrichment-analysis
4
ProprietaryPlatforms
4
WorkflowStep
3
Metagenomics
3
gene-expression
3
genomics
3
r-package
3
GenomicVariation
3
rna-seq
3
enrichment
3
MassSpectrometry
3
Cheminformatics
3
MethylSeq
3
MicroRNAArray
3
single-cell
3
ExonArray
3
Infrastructure
3
MotifAnnotation
2
pathway-enrichment-analysis
2
MotifDiscovery
2
networks
2
HistoneModification
2
PooledScreens
2
CRISPR
2
BioCarta
2
miRNA
2
rna-seq-analysis
2