hypeR：一个用于基因集富集工作流程的 R 包。
hypeR: an R package for geneset enrichment workflows.
机构信息
Bioinformatics Department, Boston University, Boston, MA 02118, USA.
Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA.
出版信息
Bioinformatics. 2020 Feb 15;36(4):1307-1308. doi: 10.1093/bioinformatics/btz700.
Abstract
SUMMARY
Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.
AVAILABILITY AND IMPLEMENTATION
The most recent version of the package is available at https://github.com/montilab/hypeR.
摘要
摘要
基因集富集是注释高通量测序数据的一种流行方法。现有的工具在提供灵活性以解决研究人员在这些分析中面临的各种挑战方面存在不足，特别是在分析多个实验中的多个特征时。我们提出了一个用于基因集富集工作流程的综合 R 包，该包除了提供分层基因集分析和内置标记报告等新功能外，还提供了多种富集、可视化和共享方法。hypeR 是为广泛的受众和用例执行基因集富集的一站式解决方案。
可用性和实现
该软件包的最新版本可在 https://github.com/montilab/hypeR 获得。
相似文献
1
hypeR: an R package for geneset enrichment workflows.hypeR：一个用于基因集富集工作流程的 R 包。
Bioinformatics. 2020 Feb 15;36(4):1307-1308. doi: 10.1093/bioinformatics/btz700.
2
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.Natrix：一个基于 SnakeMake 的工作流程，用于处理、聚类和分类分配扩增子测序reads。
BMC Bioinformatics. 2020 Nov 16;21(1):526. doi: 10.1186/s12859-020-03852-4.
3
Nanopype: a modular and scalable nanopore data processing pipeline.纳米管道：一个模块化且可扩展的纳米孔数据处理管道。
Bioinformatics. 2019 Nov 1;35(22):4770-4772. doi: 10.1093/bioinformatics/btz461.
4
PyGNA: a unified framework for geneset network analysis.PyGNA：一个用于基因集网络分析的统一框架。
BMC Bioinformatics. 2020 Oct 22;21(1):476. doi: 10.1186/s12859-020-03801-1.
5
netGO: R-Shiny package for network-integrated pathway enrichment analysis.netGO：用于网络集成通路富集分析的 R-Shiny 软件包。
Bioinformatics. 2020 May 1;36(10):3283-3285. doi: 10.1093/bioinformatics/btaa077.
6
mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data.mutscan-a 灵活的 R 包，用于高效地端到端分析变异效应数据的多路分析。
Genome Biol. 2023 Jun 1;24(1):132. doi: 10.1186/s13059-023-02967-0.
7
CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies.CTDquerier：一个用于提取、可视化和富集比较毒理学基因组学数据库（Comparative Toxicogenomics DatabaseTM）中环境和毒理学研究数据的 Bioconductor R 包。
Bioinformatics. 2018 Sep 15;34(18):3235-3237. doi: 10.1093/bioinformatics/bty326.
8
systemPipeR: NGS workflow and report generation environment.systemPipeR：二代测序工作流程与报告生成环境。
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0.
9
SoFIA: a data integration framework for annotating high-throughput datasets.SoFIA：一个用于注释高通量数据集的数据集成框架。
Bioinformatics. 2016 Sep 1;32(17):2590-7. doi: 10.1093/bioinformatics/btw302. Epub 2016 May 13.
10
Kronos: a workflow assembler for genome analytics and informatics.Kronos：一个用于基因组分析和信息学的工作流组装器。
Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
引用本文的文献
1
A stem cell differentiation model reveals two alternative fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation.一种干细胞分化模型揭示了在CBFA2T3::GLIS2驱动的急性巨核细胞白血病起始过程中的两种不同命运。
Commun Biol. 2025 Aug 27;8(1):1289. doi: 10.1038/s42003-025-08730-4.
2
Time-resolved miRNA-mRNA integrated analysis reveals the miRNA-mRNA networks underlying plasma membrane damage-dependent senescence and DNA damage response-dependent senescence in WI-38 normal human fibroblasts.时间分辨miRNA-mRNA整合分析揭示了WI-38正常人成纤维细胞中质膜损伤依赖性衰老和DNA损伤反应依赖性衰老背后的miRNA-mRNA网络。
RNA Biol. 2025 Dec;22(1):1-19. doi: 10.1080/15476286.2025.2551299. Epub 2025 Aug 29.
3
Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies.在长寿家族和综合长寿组学研究中确定的年龄和生存的全血转录特征。
bioRxiv. 2025 Jul 18:2025.07.15.664976. doi: 10.1101/2025.07.15.664976.
4
LSGI: interpretable spatial gradient analysis for spatial transcriptomics data.LSGI：用于空间转录组学数据的可解释空间梯度分析
Genome Biol. 2025 Aug 8;26(1):238. doi: 10.1186/s13059-025-03716-1.
5
Poltergeist-Like 2 (PLL2)-dependent activation of herbivore defence distinguishes systemin from other immune signalling pathways.依赖于闹鬼样蛋白2（PLL2）的食草动物防御激活将系统素与其他免疫信号通路区分开来。
Nat Plants. 2025 Jul 4. doi: 10.1038/s41477-025-02040-7.
6
CREM is a regulatory checkpoint of CAR and IL-15 signalling in NK cells.CREM是自然杀伤细胞中CAR和IL-15信号传导的一个调节检查点。
Nature. 2025 Jun 4. doi: 10.1038/s41586-025-09087-8.
7
Development and Validation of an Extracellular Matrix Gene Expression Signature for Prognostic Prediction in Patients with Uveal Melanoma.葡萄膜黑色素瘤患者预后预测的细胞外基质基因表达特征的开发与验证
Int J Mol Sci. 2025 May 1;26(9):4317. doi: 10.3390/ijms26094317.
8
Emulsion adjuvant-induced uric acid release modulates optimal immunogenicity by targeting dendritic cells and B cells.乳剂佐剂诱导的尿酸释放通过靶向树突状细胞和B细胞来调节最佳免疫原性。
NPJ Vaccines. 2025 Apr 16;10(1):72. doi: 10.1038/s41541-025-01130-z.
9
Genetic and epigenetic correlation between diabetic retinopathy and polycystic ovarian syndrome: in-silico analyses-experimental research.糖尿病视网膜病变与多囊卵巢综合征之间的遗传和表观遗传相关性：计算机模拟分析-实验研究
Ann Med Surg (Lond). 2025 Feb 6;87(3):1295-1300. doi: 10.1097/MS9.0000000000002970. eCollection 2025 Mar.
10
Sex Differences in the Cancer Proteome.癌症蛋白质组中的性别差异。
bioRxiv. 2025 Mar 17:2025.03.14.643396. doi: 10.1101/2025.03.14.643396.
本文引用的文献
1
The Reactome Pathway Knowledgebase.Reactome 通路知识库。
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132.
2
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.Enrichr：一个全面的基因集富集分析网络服务器2016年更新版。
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3.
3
clusterProfiler: an R package for comparing biological themes among gene clusters.clusterProfiler：一个用于比较基因簇间生物学主题的 R 包。
OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.
4
Molecular signatures database (MSigDB) 3.0.分子特征数据库（MSigDB）3.0。
Bioinformatics. 2011 Jun 15;27(12):1739-40. doi: 10.1093/bioinformatics/btr260. Epub 2011 May 5.
Zotero 插件