使用Bioconductor编排高通量基因组分析。
Orchestrating high-throughput genomic analysis with Bioconductor.
作者信息
Huber Wolfgang, Carey Vincent J, Gentleman Robert, Anders Simon, Carlson Marc, Carvalho Benilton S, Bravo Hector Corrada, Davis Sean, Gatto Laurent, Girke Thomas, Gottardo Raphael, Hahne Florian, Hansen Kasper D, Irizarry Rafael A, Lawrence Michael, Love Michael I, MacDonald James, Obenchain Valerie, Oleś Andrzej K, Pagès Hervé, Reyes Alejandro, Shannon Paul, Smyth Gordon K, Tenenbaum Dan, Waldron Levi, Morgan Martin
机构信息
European Molecular Biology Laboratory, Heidelberg, Germany.
1] Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Harvard School of Public Health, Boston, Massachusetts, USA.
出版信息
Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252.
Abstract
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.
摘要
Bioconductor是一个用于基因组学和分子生物学中高通量数据的分析与理解的开源、开放式开发软件项目。该项目旨在促进跨学科研究、合作以及科学软件的快速开发。基于统计编程语言R，Bioconductor由众多不同领域的科学家贡献的934个可互操作的软件包组成。这些软件包涵盖了一系列生物信息学和统计应用。它们经过正式的初步审查和持续的自动化测试。我们为潜在用户和贡献者提供一个概述。
相似文献
1
Orchestrating high-throughput genomic analysis with Bioconductor.使用Bioconductor编排高通量基因组分析。
Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252.
2
An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.用于 Bioconductor 库的直观 Python 接口展示了语言翻译器的实用性。
BMC Bioinformatics. 2010 Dec 21;11 Suppl 12(Suppl 12):S11. doi: 10.1186/1471-2105-11-S12-S11.
3
Using R and Bioconductor in Clinical Genomics and Transcriptomics.使用 R 和 Bioconductor 进行临床基因组学和转录组学研究。
J Mol Diagn. 2020 Jan;22(1):3-20. doi: 10.1016/j.jmoldx.2019.08.006. Epub 2019 Oct 9.
4
Codelink: an R package for analysis of GE healthcare gene expression bioarrays.Codelink：一个用于分析通用电气医疗集团基因表达生物芯片的R软件包。
Bioinformatics. 2007 May 1;23(9):1168-9. doi: 10.1093/bioinformatics/btm072. Epub 2007 Mar 7.
5
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.GEOquery：基因表达综合数据库（GEO）与生物导体（BioConductor）之间的桥梁。
Bioinformatics. 2007 Jul 15;23(14):1846-7. doi: 10.1093/bioinformatics/btm254. Epub 2007 May 12.
6
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.单通道图形用户界面：一个用于生物导体工具的图形界面，专为不熟悉R语言的生命科学家设计。
Bioinformatics. 2007 Dec 15;23(24):3406-8. doi: 10.1093/bioinformatics/btm469. Epub 2007 Sep 17.
7
Computational methods for evaluation of cell-based data assessment--Bioconductor.基于细胞数据评估的计算方法评估——Bioconductor。
Curr Opin Biotechnol. 2013 Feb;24(1):105-11. doi: 10.1016/j.copbio.2012.09.003. Epub 2012 Oct 10.
8
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.DNAshapeR：一个用于DNA形状预测和特征编码的R/Bioconductor软件包。
Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.
9
Orchestrating single-cell analysis with Bioconductor.使用 Bioconductor 进行单细胞分析的协调。
Nat Methods. 2020 Feb;17(2):137-145. doi: 10.1038/s41592-019-0654-x. Epub 2019 Dec 2.
10
Sharing Programming Resources Between Bio* Projects.生物相关项目间的编程资源共享。
Methods Mol Biol. 2019;1910:747-766. doi: 10.1007/978-1-4939-9074-0_25.
引用本文的文献
1
A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.中国西北部地区乙型肝炎病毒相关肝硬化患者肠道微生物群的宏基因组关联研究。
Front Genet. 2025 Aug 20;16:1619911. doi: 10.3389/fgene.2025.1619911. eCollection 2025.
2
Thermoneutral housing worsens MASLD and reveals defective brown adipose tissue response to β3-adrenergic stimulation.热中性环境会使代谢相关脂肪性肝病恶化，并揭示棕色脂肪组织对β3-肾上腺素能刺激的反应存在缺陷。
iScience. 2025 Jul 26;28(9):113221. doi: 10.1016/j.isci.2025.113221. eCollection 2025 Sep 19.
3
Transcriptional reprogramming of Novacetimonas hansenii SI1 during growth on glycerol.甘油生长过程中汉氏新醋杆菌SI1的转录重编程
Appl Microbiol Biotechnol. 2025 Sep 2;109(1):194. doi: 10.1007/s00253-025-13583-2.
4
miR-361-5p contributes to the pathogenesis of Alzheimer's disease.微小RNA-361-5p促成阿尔茨海默病的发病机制。
Sci Rep. 2025 Aug 23;15(1):31046. doi: 10.1038/s41598-025-17112-z.
5
IWS1 positions downstream DNA to globally stimulate Pol II elongation.IWS1将下游DNA定位，以全局刺激RNA聚合酶II的延伸。
Nat Commun. 2025 Aug 20;16(1):7747. doi: 10.1038/s41467-025-62913-5.
6
DeepGraphMut: a graph-based deep learning method for cancer prognosis using somatic mutation profile.深度图突变分析（DeepGraphMut）：一种基于图的深度学习方法，用于利用体细胞突变谱预测癌症预后。
Brief Bioinform. 2025 Jul 2;26(4). doi: 10.1093/bib/bbaf409.
7
Dosing and Serostatus Shape the Efficacy of Adenovirus, mRNA, and Protein Vaccines.剂量和血清状态决定腺病毒疫苗、mRNA疫苗和蛋白质疫苗的效力。
bioRxiv. 2025 Jul 17:2025.07.16.665159. doi: 10.1101/2025.07.16.665159.
8
scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.scplainer：使用线性模型理解基于质谱的单细胞蛋白质组学数据。
Genome Biol. 2025 Aug 7;26(1):237. doi: 10.1186/s13059-025-03713-4.
9
The Computer-Assisted Sequence Annotation (CASA) workflow for enzyme discovery.用于酶发现的计算机辅助序列注释（CASA）工作流程。
Appl Plant Sci. 2025 Jun 3;13(4):e70009. doi: 10.1002/aps3.70009. eCollection 2025 Jul-Aug.
10
Functional genomics of trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense across multiple time points and tissues.在多个时间点和组织中感染刚果锥虫的耐锥虫和易感染锥虫的牛的功能基因组学
PLoS Negl Trop Dis. 2025 Aug 4;19(8):e0012882. doi: 10.1371/journal.pntd.0012882. eCollection 2025 Aug.
本文引用的文献
1
Scalable Genomics with R and Bioconductor.使用R和生物导体进行可扩展基因组学研究。
Stat Sci. 2014 May;29(2):214-226. doi: 10.1214/14-STS476. Epub 2014 Aug 18.
2
OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.OpenCyto：一个用于可扩展、稳健、可重复且自动化的端到端流式细胞术数据分析的开源基础设施。
PLoS Comput Biol. 2014 Aug 28;10(8):e1003806. doi: 10.1371/journal.pcbi.1003806. eCollection 2014 Aug.
3
Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis.通过整合蛋白质组、转录组和 DNA 甲基化组分析鉴定造血干细胞及其早期祖细胞中的调控网络。
Cell Stem Cell. 2014 Oct 2;15(4):507-522. doi: 10.1016/j.stem.2014.07.005. Epub 2014 Aug 21.
4
Epiviz: interactive visual analytics for functional genomics data.Epiviz：功能基因组学数据的交互式可视化分析。
Nat Methods. 2014 Sep;11(9):938-40. doi: 10.1038/nmeth.3038. Epub 2014 Aug 3.
5
Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.通过对 1525 例患者样本的荟萃分析预测晚期卵巢癌的风险。
J Natl Cancer Inst. 2014 Apr 3;106(5):dju048. doi: 10.1093/jnci/dju048.
6
Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.晚期卵巢癌预后基因标志物的比较性荟萃分析。
J Natl Cancer Inst. 2014 Apr 3;106(5):dju049. doi: 10.1093/jnci/dju049.
7
Waste not, want not: why rarefying microbiome data is inadmissible.不浪费，不匮乏：为何微生物组数据稀疏化不可取。
PLoS Comput Biol. 2014 Apr 3;10(4):e1003531. doi: 10.1371/journal.pcbi.1003531. eCollection 2014 Apr.
8
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.VariantAnnotation：一个用于探索和注释遗传变异的 Bioconductor 软件包。
Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.
9
Credit for code.代码来源。
Nat Genet. 2014 Jan;46(1):1. doi: 10.1038/ng.2869.
10
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages.细胞间表达变异性随后的信号强化逐渐分离早期小鼠谱系。
Nat Cell Biol. 2014 Jan;16(1):27-37. doi: 10.1038/ncb2881. Epub 2013 Dec 1.
Zotero 插件