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...
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...
2021 STAT115 Chapter 5.6 Gene Set Enrichment Analyses 20:53 2021 STAT115 Lab2.1 STAR Tutorial 26:18 2021 STAT115 Lab2.2 RSeQC Tutorial 26:24 2021 STAT115 Lab2.3 RSEM/Salmon Tutorial 21:22 2021 STAT115 Chapter 6.1/2 Hierarchical Clustering 20:58 2021 STAT115 Chapter 6.3 K-means Clus...
To test the relationship between coexpression clusters and IBD disease susceptibility loci we performed gene-set enrichment analysis using MAGMA (Multi-marker Analysis of GenoMic Annotation) (de Leeuw et al. 2015). Amongst the clusters with > 100 transcripts, we detected significant (pMAGMA...
Bar Plot Dot Plot Enrichment Plot Map Enriched GO induced graph (goplot, GO only) Enriched GO induced graph (cnetplot) Pathview Plots (KEGG) Acknowledgements: GuangchuangYu/clusterProfiler Mohammed Khalfan - Gene Set Enrichment Tutorial
摘要: This is the tutorial for the exercises on day 4 of the course on Practical DNA Microarray Analysis. Topics are gene set enrichment methods introduced by Lamb et al. (2003) and a global test introduced by Goeman et al. (2004)
Workflow analysisCell identity characterizationTranscriptomic signaturesGene set enrichment approachDendritic cells (DCs) are immune sentinels of the body and play a key role in the orchestration of the communication between the innate and the adaptive immune systems. DCs can polarize innate and adaptive ...
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...
Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain ABSTRACT Motivation: Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale fun...
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...