Biocview "GeneSetEnrichment"

Acid Genomics GSEA
Acid Genomics GSEA
Acid Genomics GSEA
Activity and Diversity Analysis Module Graphical User Interface
Activity and Diversity Analysis Module Graphical User Interface
ADAM: Activity and Diversity Analysis Module
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
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 using Multiple Corespondence Analysis
Analysis routines over a FacileDataStore
Analysis routines over a FacileDataStore
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 Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
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
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 Geneset Enrichment Workflows
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
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
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
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
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
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
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
Biological Network Analysis
Biological Network Analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Category Analysis
Category Analysis
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Chromosmal Aberrations Finder in Expression data
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
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
Combining GSEA-based pathway enrichment with multi omics data integration
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Companion package to chipenrich
Comprehensive analysis of transciptome data
Comprehensive analysis of transcriptome data
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)
Data package for query/retrieval of species specific MSigDB versions
Data package for query/retrieval of species specific MSigDB versions
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
dgeAnalysis
Differential Epigenetic Coregulation Test
Differential Expression Analysis for RNA-seq data through a robust variance component test
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
Easy enrichment testing for multiple terms over a background
Easy single cell analysis platform for enrichment
Empirical Analysis of Digital Gene Expression Data in R
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Exploration and Significant Biology on a Gene Set.
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment 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
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 Enrichment analysis
Functional Enrichment analysis
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 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 ontology enrichment using FUNC
Generally Applicable Gene-set Enrichment for Pathway Analysis
Gene regulator enrichment analysis
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 (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
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 / Projection Displays
Gene Set Enrichment / Projection Displays
Gene-set Enrichment with Regularized Regression
Gene-set Enrichment with Regularized Regression
GeneSet objects from ChIP-Seq experiments
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation Index
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
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
HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data
Hyper Enrichment
Identification of candidate causal perturbations from differential gene expression data
Identification of candidate causal perturbations from differential gene expression data
Identify Moonlighting ncRNAs
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
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 Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Statistics of alleLe Dependent Expression
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Iterative Binary Biclustering of Genesets
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
Learn and Apply Cell Type Signatures
Learn and Apply Cell Type Signatures
Linear Models for Microarray Data
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
Make Sense to Gene Set Enrichment Analysis Outputs
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 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
Microarray Analysis of Differential Expression
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-based gene set analysis
Model-based gene set analysis
MulEA - A Tool for Multi Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multivariate and directional gene set testing
Multivariate and directional gene set testing
netboxr
netboxr
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
PatchseqMap
Pathway Association Study Tool (PAST)
Pathway Association Study Tool (PAST)
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)
pinnacle: Gene set enrichment analysis based on genomic intervals
Pipeline for augmented co-expression analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Provides shiny components to visualize multilGSEA results
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
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
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
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
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
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
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package of gene set enrichment analysis
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
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 Prognostic Signatures
Significance Analysis of Prognostic Signatures
Simplified RNA-Seq Analysis Pipeline
Simplify Functional Enrichment Results
Simplify Functional Enrichment Results
Single-Cell Operation for Neat Enrichment
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
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
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
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 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
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
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
Visualization of Functional Enrichment Result
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)