Biocview "GeneSetEnrichment"

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Activity and Diversity Analysis Module Graphical User Interface

ADAM: Activity and Diversity Analysis Module

A Framework for visualizing gene set enrichment throughout neurodevelopment

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

Analysing Illumina HumanMethylation BeadChip Data

analysis of co-regulatory network motifs and inference of 'dual regulons'.

Analysis of single-cell epigenomics datasets with a Shiny App

Analytical R tools for Mass Spectrometry

Analyze Gene Sets Collections Properites

Analyze Transcription Factor Enrichment

An integrated analysis package of miRNA and mRNA expression data

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

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 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

askoR - Differential Expresion Analysis using edgeR

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

A Tool for Generic Cell Type Enrichment Analysis

a tool set for pathway based data integration and visualization

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)

A unified interface to a plethora of gene set enrichment analysis methods

A universal enrichment tool for interpreting omics data

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

Biological Network Analysis

BLMA: A package for bi-level meta-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 the Reactome Analysis Service for comparative multi-omics gene set analysis

Clustering of Time Series Gene Expression data

Codon Usage Analysis and Prediction of Gene Expressivity

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

Competitive Balances for Taxonomic Enrichment Analysis in R

Comprehensive analysis of transciptome data

Comprehensive analysis of transcriptome data

Coordinated Gene Activity in Pattern Sets

Creation and Analysis of Pathway Expression Profiles (PEPs)

Data package for query/retrieval of species specific MSigDB versions

Detection of miRNAs that regulate interacting groups of pathways

Detect tissue heterogeneity in expression profiles with gene sets

dgeAnalysis

Differential cell type change analysis using Logistic/linear Regression

Differential Epigenetic Coregulation Test

Differential Expression Analysis for RNA-seq data through a robust variance component test

Discriminant Analysis for Evolutionary Inference

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

Efficient, Scalable, and Reproducible Enrichment Workflows

Empirical Analysis of Digital Gene Expression Data in R

Engineering Evaluation by Gene Categorization (eegc)

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis for Gene Ontology

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Ensemble of Gene Set Enrichment Analyses

Estimate Systems Immune Response from RNA-seq data

EWCE for Multiple Gene Lists

Exploration and Significant Biology on a Gene Set.

Expression Weighted Celltype Enrichment

Fast Gene Set Enrichment Analysis

Fast Permutation-based Gene Set Analysis

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

fedupShiny

Find the most characteristic gene ontology terms for groups of human genes

Fisher's Test for Enrichment and Depletion of User-Defined Pathways

Functional analysis of metabolic and transcriptomic data

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

Gene Expression Atlas query and gene set enrichment package.

Gene expression changes in three biological conditions

Gene expression enrichment in human brain regions

Gene ontology enrichment using FUNC

Generally Applicable Gene-set Enrichment for Pathway Analysis

Generation of null ranges via bootstrapping or covariate matching

Gene regulator enrichment analysis

Gene set analysis following differential expression using linear (mixed) modeling with dream

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 Enrichment Analysis Extended to Contingency Cubes

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Gene Set Enrichment Analysis with Networks

Geneset enrichment based on InterPro domain signatures

Gene set enrichment data structures and methods

Gene Set Enrichment For ChIP-seq Peak Data

Gene Set Enrichment Meta-Analysis

Gene Set Enrichment / Projection Displays

Gene-set Enrichment with Regularized Regression

GeneSet objects from ChIP-Seq experiments

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

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

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

GREAT Analysis - Functional Enrichment on Genomic Regions

HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Identification of candidate causal perturbations from differential gene expression data

Identify Moonlighting ncRNAs

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 miRNA sponge modules in heterogeneous data

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Interactive Differential Expression AnaLysis

Investigate iLINCS for candidate repurposable drugs

Iterative Binary Biclustering of Genesets

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Learn and Apply Cell Type Signatures

Linear Models for Microarray Data

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Locus overlap analysis for enrichment of genomic ranges

Make Biological Sense of Gene Set Enrichment Analysis Outputs

Massive and Integrative Gene Set Analysis

Metabolite Set Enrichment Analysis (MSEA)

Methods to Find Pathways with Significantly Different Variability

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 gene set analysis

Modularized and interactive analyses over a FacileDataStore

Multi-Contrast Gene Set Enrichment Analysis

Multi Dimensional Gene Set Analysis.

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multi-Omics integration and VIsualization in Cancer Subtyping

Multi-Scale Target Explorer

Multivariate and directional gene set testing

netboxr

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Open Cancer TherApeutic Discovery (OCTAD)

Outlier profile and pathway analysis in R

Overlay omics data onto SBGN pathway diagram

Package for CTDbase data query, visualization and downstream analysis

PatchseqMap

Pathway Association Study Tool (PAST)

PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Pipeline for augmented co-expression analysis

Platform for integrative analysis of omics data

plot bayesian network inferred from gene expression data based on enrichment analysis results

Plot Gene Ontology and KEGG pathway Annotation and Abundance

Polygenic Pathway Enrichment Accounting for Genetic Linkage

Provides shiny components to visualize multilGSEA results

Provides shiny modules to visualize sparrow results

Putting the fun in LINCS L1000 data analysis

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

qusage: Quantitative Set Analysis for Gene Expression

Random Gene Set Enrichment Analysis

Rank-based signature enrichment analysis for single-cell data

Rank-based single-sample gene set scoring method

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 list of genes or genomic regions

Reactome Pathway Analysis

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Reproducible GSEA Benchmarking

R Interface with InterMine-Powered Databases

RNA-binding protein motif analysis

RNA Centric Annotation System

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

R-side access to published microbial signatures from BugSigDB

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Seamless navigation through combined results of set-based and network-based enrichment analysis

Signature Overrepresentation Analysis

Significance Analysis of Function and Expression

Significance Analysis of Prognostic Signatures

Simplified RNA-Seq Analysis Pipeline

Simplify Functional Enrichment Results

Single-Cell Operation for Neat Enrichment

Single Cell - R Analysis Toolbox

SISPA: Method for Sample Integrated Set Profile Analysis

statistical analysis and visualization of functional profiles for genes and gene clusters

Statistical Analysis of the GeneChip

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Suite of Functions for Pooled Crispr Screen QC and Analysis

Survival analysis using transcriptional networks inferred by the RTN package

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Take command of set enrichment analyses through a unified interface

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Tissue-specific gene enrichment analysis

Tokenizing Text of Gene Set Enrichment Analysis

Tools for making reports in various formats

Tools for manipulating GO and microarrays

Tools for Manipulating the FOBI Ontology

Transcriptional analysis based on transcriptograms

Transcriptomic Ovarian Cancer Datasets

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

Unified statistal Modeling of Omics Data

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

Visualising Set Enrichment Analysis Results

Visualization of Functional Enrichment Result

What the Package Does (One Line, Title Case)

Workflow for constructing Pathway-Gene-Transcript expression networks

Biocview "GeneSetEnrichment"

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