{"title":"scToppR: ToppGene 的编码友好 R 接口。","authors":"Bryan Granger, Stefano Berto","doi":"10.1093/bioinformatics/btae582","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>The scToppR package provides a ToppGene interface from R programs/scripts to fully access/control the database for functional enrichment without the need for active interaction on its Web site (https://toppgene.cchmc.org/).</p><p><strong>Results: </strong>The library facilitates the functional enrichment analysis and visualization by interacting with ToppGene, downloading the functional enrichment dataframes, and using R environment to visualize the final results.</p><p><strong>Availability and implementation: </strong>Code and documentation are currently available at https://github.com/BioinformaticsMUSC/scToppR.</p>","PeriodicalId":93899,"journal":{"name":"Bioinformatics (Oxford, England)","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552619/pdf/","citationCount":"0","resultStr":"{\"title\":\"scToppR: a coding-friendly R interface to ToppGene.\",\"authors\":\"Bryan Granger, Stefano Berto\",\"doi\":\"10.1093/bioinformatics/btae582\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Motivation: </strong>The scToppR package provides a ToppGene interface from R programs/scripts to fully access/control the database for functional enrichment without the need for active interaction on its Web site (https://toppgene.cchmc.org/).</p><p><strong>Results: </strong>The library facilitates the functional enrichment analysis and visualization by interacting with ToppGene, downloading the functional enrichment dataframes, and using R environment to visualize the final results.</p><p><strong>Availability and implementation: </strong>Code and documentation are currently available at https://github.com/BioinformaticsMUSC/scToppR.</p>\",\"PeriodicalId\":93899,\"journal\":{\"name\":\"Bioinformatics (Oxford, England)\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-11-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552619/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics (Oxford, England)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/bioinformatics/btae582\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics (Oxford, England)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btae582","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
动机scToppR软件包为R程序/脚本提供了一个ToppGene接口，以便完全访问/控制功能富集数据库，而无需在其网站（https://toppgene.cchmc.org/）上进行主动交互。结果：该库通过与ToppGene交互，下载功能富集数据帧，并使用R环境将最终结果可视化，促进了功能富集分析和可视化：该库通过与 ToppGene 交互、下载功能富集数据帧以及使用 R 环境对最终结果进行可视化，促进了功能富集分析和可视化：代码和文档目前可从 https://github.com/BioinformaticsMUSC/scToppR.Supplementary 信息中获取：补充数据可在 Bioinformatics online 上获取。
scToppR: a coding-friendly R interface to ToppGene.
Motivation: The scToppR package provides a ToppGene interface from R programs/scripts to fully access/control the database for functional enrichment without the need for active interaction on its Web site (https://toppgene.cchmc.org/).
Results: The library facilitates the functional enrichment analysis and visualization by interacting with ToppGene, downloading the functional enrichment dataframes, and using R environment to visualize the final results.
Availability and implementation: Code and documentation are currently available at https://github.com/BioinformaticsMUSC/scToppR.
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