GSEApy: Gene Set Enrichment Analysis in Python. Release notes:https://github.com/zqfang/GSEApy/releases Tutorial for scRNA-seq datasets Tutorial for general usage Citation Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python...
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework...
(2023). GOAT: efficient and robust identification of gene set enrichment. https://doi.org/10.1101/2023.12.10.570979. Contents Online tool Installing the R package Quickstart Tutorial: using the GOAT R package Preparing your gene list as input for GOAT Gene set simplification Online tool This ...
and expression values below 0.1 are set to 0.ML,FC, andPCCrepresent the maximum expression level, fold change of expression, and expression pattern correlation of gene pairs, respectively. The indexesa,b, andcare set to 1, 1, and 4 by default, which are derived from broad test.d,f,h,...
Many other gene set enrichment analysis tools have been developed in recent years following the original concept [1]. However, many of such enrichment analysis tools focus on performing enrichment using only the Gene Ontology resource [6]. In addition, enrichment analysis tools most commonly use ...
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102:15545–50. Article CAS PubMed PubMed Central Google Scholar Cun Y, Fröhlich H. Prognostic gene signatures for patient stratification in breast cancer: accuracy...
Gene functional analysis We used a variety of methods to analyze the biological significance of PluriUp and PluriPlus gene sets. Gene Set Enrichment Analysis (GSEA, [29]) takes gene sets, an expression dataset, and phenotype labels as input, and computes enrichment scores of each gene set for...
et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005). Article CAS PubMed PubMed Central Google Scholar Wang, K., Li, M. & Bucan, M. Pathway-based approaches for analysis of...
Many other gene set enrichment analysis tools have been developed in recent years following the original concept [1]. However, many of such enrichment analysis tools focus on performing enrichment using only the Gene Ontology resource [6]. In addition, enrichment analysis tools most commonly use ...
fgseais an R-package for fast preranked gene set enrichment analysis (GSEA). This package allows to quickly and accurately calculate arbitrarily low GSEA P-values for a collection of gene sets. P-value estimation is based on an adaptive multi-level split Monte-Carlo scheme. Seethe preprintfor...