CoSIA：用于 CrOss 物种调查和分析的 R Bioconductor 软件包

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Bioinformatics Pub Date : 2023-12-18 DOI:10.1093/bioinformatics/btad759

Anisha Haldar, Vishal H Oza, Nathaniel S DeVoss, Amanda D Clark, Brittany N Lasseigne

{"title":"CoSIA：用于 CrOss 物种调查和分析的 R Bioconductor 软件包","authors":"Anisha Haldar, Vishal H Oza, Nathaniel S DeVoss, Amanda D Clark, Brittany N Lasseigne","doi":"10.1093/bioinformatics/btad759","DOIUrl":null,"url":null,"abstract":"Summary High throughput sequencing technologies have enabled cross-species comparative transcriptomic studies; however, there are numerous challenges for these studies due to biological and technical factors. We developed CoSIA (Cross-Species Investigation and Analysis), an Bioconductor R package and Shiny app that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression data from Bgee across tissues and species (human, mouse, rat, zebrafish, fly, and nematode) through visualization of variability, diversity, and specificity metrics. Availability and Implementation https://github.com/lasseignelab/CoSIA Supplementary information See Supplementary Material","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":null,"pages":null},"PeriodicalIF":4.4000,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis\",\"authors\":\"Anisha Haldar, Vishal H Oza, Nathaniel S DeVoss, Amanda D Clark, Brittany N Lasseigne\",\"doi\":\"10.1093/bioinformatics/btad759\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Summary High throughput sequencing technologies have enabled cross-species comparative transcriptomic studies; however, there are numerous challenges for these studies due to biological and technical factors. We developed CoSIA (Cross-Species Investigation and Analysis), an Bioconductor R package and Shiny app that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression data from Bgee across tissues and species (human, mouse, rat, zebrafish, fly, and nematode) through visualization of variability, diversity, and specificity metrics. Availability and Implementation https://github.com/lasseignelab/CoSIA Supplementary information See Supplementary Material\",\"PeriodicalId\":8903,\"journal\":{\"name\":\"Bioinformatics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2023-12-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/bioinformatics/btad759\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad759","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

摘要

摘要高通量测序技术使跨物种比较转录组研究成为可能；然而，由于生物和技术因素，这些研究面临着诸多挑战。我们开发了 CoSIA（跨物种调查与分析），它是一个 Bioconductor R 软件包和 Shiny 应用程序，通过可视化的变异性、多样性和特异性指标，为来自 Bgee 的跨组织和物种（人、小鼠、大鼠、斑马鱼、苍蝇和线虫）非疾病野生型 RNA 测序基因表达数据的跨物种转录组比较提供了一个替代框架。可用性和实施 https://github.com/lasseignelab/CoSIA 补充信息见补充材料

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis

Summary High throughput sequencing technologies have enabled cross-species comparative transcriptomic studies; however, there are numerous challenges for these studies due to biological and technical factors. We developed CoSIA (Cross-Species Investigation and Analysis), an Bioconductor R package and Shiny app that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression data from Bgee across tissues and species (human, mouse, rat, zebrafish, fly, and nematode) through visualization of variability, diversity, and specificity metrics. Availability and Implementation https://github.com/lasseignelab/CoSIA Supplementary information See Supplementary Material

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.