Gene Set Enrichment AnalysisBlackhurst, Isaac
一、fgsea包,fgsea是Fast Gene Set Enrichment Analysis的缩写 1. 首先需要准备好rank文件,就是排好序的基因列表文件。一般做完差异表达分析都能得到这样一个文件。第一列是entrez gene id号,第二列可以是t值,也可以是foldchange。 代码语言:javascript ...
Stiglic G, Bajgot M, Kokol P (2010) Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays. BMC Bioinformatics 11: 176.Stiglic Gregor, Mateja Bajgot,Kokol Peter.Gene set enrichment meta-learning analysis:next-genera- tion sequencing versus microarrays[J].BMC...
Gene set/pathway enrichment analysis. Methods in Molecular Biology, 2013, 939, 201-213.Hung J. H. Gene Set/Pathway enrichment analysis . Methods Mol. Biol. 939 , 201–213 (2013).Hung,J.H. (2013) Gene Set/Pathway enrichment analysis. Methods Mol. Biol., 939, 201-213....
GSEA(Gene Set Enrichment Analysis),该方法发表于2005年的Gene set enrichment analysis: a knowledge-based approach forinterpreting genome-wide expression profiles,是一种基于基因集的富集分析方法,在对基因表达数据分析时,首先确定分析的目的,即选择MSigDB中的一个或多个功能基因集进行分析(基因矩阵转置文件格式(*...
Gene Set Enrichment Analysis( GSEA )是一种基于基因功能 / 通路的富集分析方法。首先基于基因表达数据的变化的大小进行排序,然后对选定的或者自定义的Gene Set进行富集,最后计算一个富集打分( ES Score),这种分析方法可以很好的对某一通路、功能进行研究,避免了直接计算P值而忽略一些重要的基因信息,同时分析是按照某...
DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primar
今天给大家分享一篇文献《Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles》,翻译一下就是,基因集富集分析:一个基于先验知识的解释全基因组表达谱的工具。这篇文章被引次数超级高,已经有35875次了。 富集分析在生信研究中运用的十分广泛,我们就从GSEA的原论...
一、fgsea包,fgsea是Fast Gene Set Enrichment Analysis的缩写 1. 首先需要准备好rank文件,就是排好序的基因列表文件。一般做完差异表达分析都能得到这样一个文件。第一列是entrez gene id号,第二列可以是t值,也可以是foldchange。 > ranksID t1 170942 -63.3370342 109711 -49.7477873 18124 -43.6387844 12775 ...
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...