Biocview "GeneSetEnrichment"

ADAM: Activity and Diversity Analysis Module
A Framework for visualizing gene set enrichment throughout neurodevelopment
A Framework for visualizing gene set enrichment throughout neurodevelopment
Analysing Illumina HumanMethylation BeadChip Data
Analysing Illumina HumanMethylation BeadChip Data
analysis of co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analysis of RNA-Seq Count Data using Multiple Corespondence Analysis
Analysis of RNA-Seq Count Data using Multiple Corespondence Analysis
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analyze Gene Sets Collections Properites
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology.
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
An R package for gene set enrichment and network analysis of various high-throughput data
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
An R package to perform the network enrichment analysis (NEA).
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
A unified interface to a plethora of gene set enrichment analysis methods
A web interface for gene-set enrichment analyses
A web interface for gene-set enrichment analyses
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Biological Network Analysis
Biological Network Analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Category Analysis
Category Analysis
Category Analysis
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Chromosmal Aberrations Finder in Expression data
Chromosmal Aberrations Finder in Expression data
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Companion package to chipenrich
Comprehensive analysis of transciptome data
Comprehensive analysis of transciptome data
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Creation and Analysis of Pathway Expression Profiles (PEPs)
Creation and Analysis of Pathway Expression Profiles (PEPs)
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Easy enrichment testing for multiple terms over a background
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Functional Gene Networks derived from biological enrichment analyses
Functional Gene Networks derived from biological enrichment analyses
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Gene Expression Atlas query and gene set enrichment package.
Gene Expression Atlas query and gene set enrichment package.
Gene expression changes in three biological conditions
Gene expression changes in three biological conditions
Gene expression enrichment in human brain regions
Gene expression enrichment in human brain regions
Gene expression enrichment in human brain regions
Gene ontology enrichment using FUNC
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment Analysis with Networks
Geneset enrichment based on InterPro domain signatures
Geneset enrichment based on InterPro domain signatures
Gene set enrichment data structures and methods
Gene set enrichment data structures and methods
Gene set enrichment data structures and methods
Gene Set Enrichment For ChIP-seq Peak Data
Gene Set Enrichment For ChIP-seq Peak Data
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
GeneSet objects from ChIP-Seq experiments
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation Index
Gene Set Regulation Index
Gene Set Variation Analysis for microarray and RNA-seq data
Gene Set Variation Analysis for microarray and RNA-seq data
Gene Set Variation Analysis for microarray and RNA-seq data
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
GISPA: Method for Gene Integrated Set Profile Analysis
GISPA: Method for Gene Integrated Set Profile Analysis
GO-function: deriving biologcially relevant functions from statistically significant functions
GO-function: deriving biologcially relevant functions from statistically significant functions
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Iterative Binary Biclustering of Genesets
Iterative Binary Biclustering of Genesets
Learn and Apply Cell Type Signatures
Linear Models for Microarray Data
Linear Models for Microarray Data
Location overlap analysis for enrichment of genomic ranges
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Metabolite Set Enrichment Analysis (MSEA)
Methods to Find Pathways with Significantly Different Variability
Methods to Find Pathways with Significantly Different Variability
Methods to Find Pathways with Significantly Different Variability
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation
Microarray Analysis of Differential Expression
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-based gene set analysis
Model-based gene set analysis
Model-based gene set analysis
MulEA - A Tool for Multi Enrichment Analysis
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multi-Omics Data Fusion for Cancer Module Discovery
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
Parameterized Fast GSEA
PatchseqMap
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
prism: Gene set enrichment analysis based on genomic intervals
Putting the fun in LINCS L1000 data analysis
Putting the fun in LINCS L1000 data analysis
Putting the fun in LINCS L1000 data analysis
Quantify and interpret divers of variation in multilevel gene expression experiments
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
Random Gene Set Enrichment Analysis
Random Gene Set Enrichment Analysis
Rank-based single-sample gene set scoring method
Rank-based single-sample gene set scoring method
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
Rapid Integration of Term Annotation and Network resources
RcisTarget: Identify transcription factor binding motifs enriched on a gene list
RcisTarget: Identify transcription factor binding motifs enriched on a gene list
Reactome Pathway Analysis
Reactome Pathway Analysis
Reactome Pathway Analysis
Reconstruction of transcriptional networks and analysis of master regulators
Reconstruction of transcriptional networks and analysis of master regulators
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
RNA-binding protein motif analysis
RNA-binding protein motif analysis
RNA Centric Annotation System
RNA Centric Annotation System
RNA Centric Annotation System
RNASeqR: RNA-Seq workflow for case-control study
RNASeqR: RNA-Seq workflow for case-control study
RNASeqR: RNA-Seq workflow for case-control study
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package of gene set enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
Simplified RNA-Seq Analysis Pipeline
Simplified RNA-Seq Analysis Pipeline
SISPA: Method for Sample Integrated Set Profile Analysis
SISPA: Method for Sample Integrated Set Profile Analysis
SISPA: Method for Sample Integrated Set Profile Analysis
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Survival analysis using transcriptional networks inferred by the RTN package
Survival analysis using transcriptional networks inferred by the RTN package
Survival analysis using transcriptional networks inferred by the RTN package
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Tissue-specific gene enrichment analysis
Tissue-specific gene enrichment analysis
Tools for making reports in various formats
Tools for making reports in various formats
Tools for making reports in various formats
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptomic Ovarian Cancer Datasets
Transcriptomic Ovarian Cancer Datasets
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result