• MADM

  • Referenced in 119 articles [sw06484]
  • Rangiranje (VIKOR), Data Envelopment Analysis (DEA), Preference Ranking METHod for Enrichment Evaluations (PROMETHEE), ELimination ... ELECTRE), COmplex PRoportional ASsessment (COPRAS), Grey Relational Analysis (GRA), UTility Additive (UTA), and Ordered Weighted...
  • GSA

  • Referenced in 37 articles [sw18747]
  • point is the interesting Gene Set Enrichment Analysis (GSEA) procedure of {it A. Subramanian...
  • Bio-PEPA

  • Referenced in 102 articles [sw01361]
  • which different kindsof analysis can be carried out. Bio-PEPA is enriched with some notions ... into thenew language and we report some analysis results...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • Gene Set Enrichment. Background: Gene set enrichment analysis (GSEA) is a microarray data analysis method ... developed a modified gene set enrichment analysis method based on a parametric statistical analysis model ... Compared with GSEA, the parametric analysis of gene set enrichment (PAGE) detected a larger number ... data irrespective of different Affymetrix probe level analysis methods or different microarray platforms. Comparison...
  • ProbCD

  • Referenced in 5 articles [sw20338]
  • ProbCD: enrichment analysis accounting for categorization uncertainty. As in many other areas of science, systems ... type of categorical data analysis known in this field as enrichment (also over-representation ... enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology ... data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature...
  • ToppGene Suite

  • Referenced in 6 articles [sw30169]
  • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. ToppGene Suite (http://toppgene.cchmc.org ... functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis...
  • GSEA-P

  • Referenced in 4 articles [sw30024]
  • desktop application for Gene Set Enrichment Analysis. Gene Set Enrichment Analysis (GSEA) is a computational...
  • GeneSigDB

  • Referenced in 4 articles [sw17287]
  • manually curated database and resource for analysis of gene expression signatures. GeneSigDB (http://www.genesigdb.org ... these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from ... file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB...
  • Enrichr

  • Referenced in 3 articles [sw17198]
  • Interactive and collaborative HTML5 gene list enrichment analysis tool. Background: System-wide profiling of genes ... into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have ... analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures ... easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries...
  • GOSim

  • Referenced in 5 articles [sw08204]
  • large amounts of biological data. During the analysis of such data often there ... offers the possibility of a GO enrichment analysis using the topGO package. Moreover, since version...
  • MAST

  • Referenced in 5 articles [sw30709]
  • variation. Our model provides gene set enrichment analysis tailored to single-cell data. It provides...
  • MSEA

  • Referenced in 2 articles [sw16938]
  • quantitative metabolomic data. Gene set enrichment analysis (GSEA) is a widely used technique in transcriptomic ... based server, called Metabolite Set Enrichment Analysis (MSEA), to help researchers identify and interpret patterns ... single sample profiling (SSP) and quantitative enrichment analysis (QEA). ORA requires only a list ... provide their own metabolite sets for enrichment analysis. The MSEA server also supports conversion between...
  • GOrilla

  • Referenced in 3 articles [sw35292]
  • exact p-value for the observed enrichment, taking threshold multiple testing into account without ... need for simulations. This enables rigorous statistical analysis of thousand of genes and thousands ... seconds. The output of the enrichment analysis is visualized as a hierarchical structure, providing ... relations between enriched GO terms. Conclusion: GOrilla is an efficient GO analysis tool with unique...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • method extensively searches for subnetworks enriched with low P-value genes in GWAS datasets. Compared ... marker analysis of GWA studies. Functional enrichment analysis and comparison with previously published methods showed...
  • DOSim

  • Referenced in 2 articles [sw18860]
  • diseases. DOSim incorporates a DO-based enrichment analysis function that can be used to explore ... independent gene set. A multilayered enrichment analysis (GO and KEGG annotation) annotation function that helps...
  • DOSE

  • Referenced in 2 articles [sw16933]
  • package for disease ontology semantic and enrichment analysis. Summary: Disease ontology (DO) annotates human genes ... gene functions in disease perspective. Enrichment analyses ... including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease...
  • GKB-FP

  • Referenced in 14 articles [sw02082]
  • author. A detailed convergence analysis is provided. The paper is enriched by many numerical results...
  • topGO

  • Referenced in 3 articles [sw31859]
  • Bioconductor/R package topGO: Enrichment Analysis for Gene Ontology. topGO package provides tools for testing...
  • HPOSim

  • Referenced in 1 article [sw16935]
  • Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology. Background ... becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing ... similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets ... also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). Conclusions: HPOSim...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • data. Background: Gene set enrichment (GSE) analysis is a popular framework for condensing information from ... this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation ... current state of the art sample-wise enrichment methods. Further, we provide examples ... utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously...