Pavian：微生物组研究和病原体鉴定的宏基因组数据分析的交互式分析。
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.
机构信息
Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
Departments of Biomedical Engineering, Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
出版信息
Bioinformatics. 2020 Feb 15;36(4):1303-1304. doi: 10.1093/bioinformatics/btz715.
Abstract
SUMMARY
Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers-such as Kraken, Centrifuge and MethaPhlAn-using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection.
AVAILABILITY AND IMPLEMENTATION
Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.
摘要
摘要
Pavian 是一个用于探索宏基因组实验分类结果的 Web 应用程序。使用 Pavian，研究人员可以使用交互式数据表、热图和 Sankey 流程图分析、可视化和转换来自各种分类器（如 Kraken、Centrifuge 和 MethaPhlAn）的结果。交互式比对覆盖视图可帮助验证与特定基因组的匹配，这在使用宏基因组实验进行病原体检测时至关重要。
可用性和实现
Pavian 是用 R 语言作为模块化的 Shiny Web 应用程序实现的，并根据 GPL-3 协议在 http://github.com/fbreitwieser/pavian 上免费提供。
相似文献
1
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.Pavian：微生物组研究和病原体鉴定的宏基因组数据分析的交互式分析。
Bioinformatics. 2020 Feb 15;36(4):1303-1304. doi: 10.1093/bioinformatics/btz715.
2
animalcules: interactive microbiome analytics and visualization in R.微生物组分析与可视化 R 语言工具包
Microbiome. 2021 Mar 28;9(1):76. doi: 10.1186/s40168-021-01013-0.
3
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.Shiny-phyloseq：用于具有溯源追踪功能的交互式微生物组分析的网络应用程序。
Bioinformatics. 2015 Jan 15;31(2):282-3. doi: 10.1093/bioinformatics/btu616. Epub 2014 Sep 26.
4
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.KrakenUniq：基于独特的 k-mer 计数实现自信且快速的宏基因组分类。
Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0.
5
RevEcoR: an R package for the reverse ecology analysis of microbiomes.RevEcoR：一个用于微生物群落逆向生态学分析的R软件包。
BMC Bioinformatics. 2016 Jul 29;17(1):294. doi: 10.1186/s12859-016-1088-4.
6
Web-igloo: a web based platform for multivariate data visualization.网络冰屋：一个基于网络的多变量数据可视化平台。
Bioinformatics. 2017 Feb 15;33(4):615-617. doi: 10.1093/bioinformatics/btw669.
7
Chordomics: a visualization tool for linking function to phylogeny in microbiomes.弦理论组学：一种将功能与微生物组系统发育联系起来的可视化工具。
Bioinformatics. 2020 Feb 15;36(4):1309-1310. doi: 10.1093/bioinformatics/btz711.
8
BioSankey: Visualization of Microbial Communities Over Time.生物桑基图：微生物群落随时间的可视化
J Integr Bioinform. 2018 Jun 13;15(4):20170063. doi: 10.1515/jib-2017-0063.
9
Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.动态评估微生物生态学 (DAME)：一个用于交互式分析和可视化微生物测序数据的网络应用程序。
Bioinformatics. 2018 Mar 15;34(6):1050-1052. doi: 10.1093/bioinformatics/btx686.
10
jHeatmap: an interactive heatmap viewer for the web.jHeatmap：一个用于网页的交互式热图查看器。
Bioinformatics. 2014 Jun 15;30(12):1757-8. doi: 10.1093/bioinformatics/btu094. Epub 2014 Feb 23.
引用本文的文献
1
RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data.RpNGS：临床宏基因组学数据中病原体鉴定与监测的自动化平台。
PeerJ. 2025 Aug 12;13:e19849. doi: 10.7717/peerj.19849. eCollection 2025.
2
Fold first, ask later: structure-informed function annotation of phage proteins.先折叠，后询问：噬菌体蛋白质的结构导向功能注释
bioRxiv. 2025 Jul 20:2025.07.17.665397. doi: 10.1101/2025.07.17.665397.
3
A targeted tiled amplicon sequencing approach for clade and subclade level differentiation of monkeypox virus from wastewater.一种用于从废水中区分猴痘病毒进化枝和亚进化枝水平的靶向平铺扩增子测序方法。
Sci Rep. 2025 Aug 11;15(1):29361. doi: 10.1038/s41598-025-13927-y.
4
Pangenome-scale annotation of mycobacteriophages for dissecting phage-host interactions based on a sequence clustering and structural homology analysis strategy.基于序列聚类和结构同源性分析策略对分枝杆菌噬菌体进行全基因组规模注释以剖析噬菌体-宿主相互作用
mSystems. 2025 Aug 19;10(8):e0050825. doi: 10.1128/msystems.00508-25. Epub 2025 Jul 29.
5
Sequencing airborne DNA to monitor crop pathogens and pests.对空气中的DNA进行测序以监测作物病原体和害虫。
iScience. 2025 Jun 16;28(7):112912. doi: 10.1016/j.isci.2025.112912. eCollection 2025 Jul 18.
6
Metagenomic analysis uncovers novel hepadnaviruses and nackednaviruses.宏基因组分析发现了新型嗜肝DNA病毒和无包膜病毒。
Sci Rep. 2025 Jul 9;15(1):24699. doi: 10.1038/s41598-025-05993-z.
7
Evaluating Good Husbandry Practices and Organic Fermented Additives for Coccidiosis Control in a Pilot Study Using Slow-Growing Broilers.在一项使用慢速生长肉鸡的试点研究中评估良好饲养管理措施和有机发酵添加剂对球虫病的控制效果
Animals (Basel). 2025 Jun 13;15(12):1752. doi: 10.3390/ani15121752.
8
Microbial populations under fluoride stress: a metagenomic exploration from Indian soil.氟胁迫下的微生物群落：来自印度土壤的宏基因组学探索
World J Microbiol Biotechnol. 2025 Jun 25;41(7):221. doi: 10.1007/s11274-025-04408-5.
9
Bacterial community composition and diversity associated with developmental stages of Anopheles subpictus.与拟态按蚊发育阶段相关的细菌群落组成和多样性
Int Microbiol. 2025 Jun 20. doi: 10.1007/s10123-025-00688-x.
10
Occurrence of Recombinant Canine Coronavirus, Picodicistrovirus, and Circovirus in Red Foxes () Implies Frequent Virus Transmission Events Among Carnivores.赤狐中重组犬冠状病毒、小双节段RNA病毒和圆环病毒的出现表明食肉动物之间频繁发生病毒传播事件。
Transbound Emerg Dis. 2025 Jun 4;2025:6681119. doi: 10.1155/tbed/6681119. eCollection 2025.
本文引用的文献
1
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.KrakenUniq：基于独特的 k-mer 计数实现自信且快速的宏基因组分类。
Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0.
2
Metaviz: interactive statistical and visual analysis of metagenomic data.Metaviz：宏基因组数据的交互式统计和可视化分析。
Nucleic Acids Res. 2018 Apr 6;46(6):2777-2787. doi: 10.1093/nar/gky136.
3
A review of methods and databases for metagenomic classification and assembly.元基因组分类和组装方法及数据库综述。
Brief Bioinform. 2019 Jul 19;20(4):1125-1136. doi: 10.1093/bib/bbx120.
4
Centrifuge: rapid and sensitive classification of metagenomic sequences.离心机：宏基因组序列的快速灵敏分类
Genome Res. 2016 Dec;26(12):1721-1729. doi: 10.1101/gr.210641.116. Epub 2016 Oct 17.
5
Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.下一代测序在神经系统感染的神经病理学诊断中的应用。
Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug.
6
MetaPhlAn2 for enhanced metagenomic taxonomic profiling.用于增强宏基因组分类分析的MetaPhlAn2
Nat Methods. 2015 Oct;12(10):902-3. doi: 10.1038/nmeth.3589.
7
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.Shiny-phyloseq：用于具有溯源追踪功能的交互式微生物组分析的网络应用程序。
Bioinformatics. 2015 Jan 15;31(2):282-3. doi: 10.1093/bioinformatics/btu616. Epub 2014 Sep 26.
8
Kraken: ultrafast metagenomic sequence classification using exact alignments.克拉肯：使用精确比对的超快速宏基因组序列分类
Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
9
D³: Data-Driven Documents.D³：数据驱动文档。
IEEE Trans Vis Comput Graph. 2011 Dec;17(12):2301-9. doi: 10.1109/TVCG.2011.185.
Zotero 插件