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 Functions
1 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 interface
4 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
enrichplot 1.24.0
Visualization of Functional Enrichment Result
3 versions - Latest release: 30 days ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data
4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.66.0
Gene set enrichment data structures and methods
3 versions - Latest release: 30 days ago - 49 dependent packages - 983 thousand downloads total - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis
3 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 analysis
2 versions - Latest release: 7 months ago - 1.03 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.32.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
3 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 data
2 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 results
1 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 App
3 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 analysis
2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.68.0
Tools for manipulating GO and microarrays
3 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 annotations
3 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 data
3 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 sets
3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.46.0
Reactome Pathway Analysis
3 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 data
3 versions - Latest release: 6 months ago - 3.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis
3 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 analysis
3 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 applications
5 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 Selection
3 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
fgsea 1.30.0
Fast Gene Set Enrichment Analysis
3 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
singscore 1.22.0
Rank-based single-sample gene set scoring method
3 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
Category 2.68.0
Category Analysis
3 versions - Latest release: 7 months ago - 13 dependent packages - 515 thousand downloads total - 1 maintainer
simplifyEnrichment 1.12.0
Simplify Functional Enrichment Results
3 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 transcriptograms
3 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 QTLs
3 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 Commons
3 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 analysis
2 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 Enrichment
3 versions - Latest release: 6 months ago - 4.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
MAST 1.28.0
Model-based Analysis of Single Cell Transcriptomics
3 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 Methylation
3 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 Data
4 versions - Latest release: 25 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
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 Analysis
3 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 Analysis
4 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 sets
3 versions - Latest release: 7 months ago - 13.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry
3 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 Analysis
3 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 Data
3 versions - Latest release: 7 months ago - 27.8 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data
3 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 Genes
2 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 Expression
3 versions - Latest release: 7 months ago - 9.18 thousand downloads total - 1 maintainer
pathVar 1.32.0
Methods to Find Pathways with Significantly Different Variability
3 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 matching
3 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 profiles
3 versions - Latest release: 7 months ago - 10.5 thousand downloads total - 1 maintainer
RITAN 1.26.0
Rapid Integration of Term Annotation and Network resources
3 versions - Latest release: 7 months ago - 9.59 thousand downloads total - 1 maintainer
GOfuncR 1.22.2
Gene ontology enrichment using FUNC
4 versions - Latest release: 3 months ago - 20.3 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
RTN 2.26.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
3 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 analysis
3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
MAGeCKFlute 2.6.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
3 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 Analysis
3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets
3 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 data
3 versions - Latest release: 7 months ago - 17.6 thousand downloads total - 1 maintainer
ttgsea 1.10.0
Tokenizing Text of Gene Set Enrichment Analysis
3 versions - Latest release: 7 months ago - 2 dependent packages - 3.68 thousand downloads total - 1 maintainer
GSRI 2.50.0
Gene Set Regulation Index
3 versions - Latest release: 7 months ago - 25.8 thousand downloads total - 1 maintainer
ADAMgui 1.18.0
Activity and Diversity Analysis Module Graphical User Interface
3 versions - Latest release: 7 months ago - 6.89 thousand downloads total - 1 maintainer
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges
3 versions - Latest release: 7 months ago - 5 dependent packages - 25 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
FGNet 3.36.0
Functional Gene Networks derived from biological enrichment analyses
3 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 Analysis
3 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 Analysis
2 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 Expressivity
3 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 Regression
3 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 MSKCC
6 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 Pipeline
3 versions - Latest release: 7 months ago - 6.15 thousand downloads total - 1 maintainer
CBEA 1.3.0
Competitive Balances for Taxonomic Enrichment Analysis in R
3 versions - Latest release: 8 months ago - 2.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
goProfiles 1.64.0
goProfiles: an R package for the statistical analysis of functional profiles
3 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 analysis
4 versions - Latest release: about 1 month ago - 4.65 thousand downloads total - 1 maintainer
TissueEnrich 1.22.0
Tissue-specific gene enrichment analysis
3 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 regression
2 versions - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
transite 1.20.1
RNA-binding protein motif analysis
4 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 Abundance
3 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 Pathways
3 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 pathways
3 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 data
3 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 set
3 versions - Latest release: 7 months ago - 9.53 thousand downloads total - 1 maintainer
oppar 1.30.0
Outlier profile and pathway analysis in R
3 versions - Latest release: 7 months ago - 10.1 thousand downloads total - 1 maintainer
oposSOM 2.20.0
Comprehensive analysis of transcriptome data
3 versions - Latest release: 7 months ago - 17.7 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
iBBiG 1.46.0
Iterative Binary Biclustering of Genesets
3 versions - Latest release: 7 months ago - 1 dependent package - 28.7 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses
4 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 package
3 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 Analysis
3 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 Module
3 versions - Latest release: 7 months ago - 1 dependent package - 7.52 thousand downloads total - 1 maintainer
RCAS 1.28.3
RNA Centric Annotation System
4 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