Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757 GSEApy is a Python/Rust implementation forGSEAand wrapper forEnrichr. ...
STAGEs: A web-based tool that integrates data visualization and pathway enrichment analysis for gene expression studies ArticleOpen access02 May 2023 reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization ArticleOpen access06...
python depict.py 1. 输出结果为多个文件,后缀为loci.txt文件保存了SNP位点对应的基因信息,内容示意如下 后缀为genesetenrichment.txt的文件保存了候选基因的基因集富集分析结果,内容示意如下 后缀为tissueenrichment.txt的文件保存了候选基因的组织/细胞富集分析结果,内容示...
Python A minimal desktop app for easy and convenient gene annotation and lookup. bioinformaticsgenegeneticslookupdesktop-applicationgene-annotationprotein-function UpdatedDec 7, 2022 JavaScript 🧬 Gene analysis toolkit based on R geneplottingenrichment-analysisid-converter ...
The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Given a list of genes, a gene ontology (GO) enrichment analysis may return hundreds of ...
Powell JA. GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. BMC Bioin- formatics 2014; 15: 146.Powell, J. A. C. GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. BMC Bioinformatics 15, 146...
The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb ...
Gene set enrichment analysis was performed on genes ranked by average CS. (D–F) SWS analysis. (D) High SWS peaks in HEL that (E) correspond to regions of genomic amplification. (F) Contiguous region of low CS genes reside in amplicon on chromosome 9p24 containing the JAK2 oncogene. See...
HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015). Article CAS Google Scholar Leek, J. T. & Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, 1724–1735 (2007). Article...
You can install the blitzGSEA Python package and its dependencies through pip by using the following command:$ pip install blitzgsea Run enrichment analysis using blitzGSEAblitzGSEA depends on two input files. 1) a gene signature and 2) a gene set library. The gene set library is a ...