Core 2: Computational Core

核心2：计算核心

• 批准号: 10153727
• 负责人: Aristotelis Tsirigos
• 金额: $ 22.5万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-12 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10153727
• 关键词: ATAC-seq; Architecture; Bioinformatics; ChIP-seq; Chromatin; Chromatin Conformation Capture and Sequencing; Collaborations; Communities; Computer Analysis; Data; Data Analyses; Data Collection; Data Set; Databases; Development; Ensure; Environment; Epigenetic Process; Genetic; Genome; Genomics; Goals; Hand; Hi-C; High Performance Computing; Infrastructure; Laboratories; Letters; Maintenance; Malignant Neoplasms; Methods; Mission; Molecular; Molecular Conformation; Neck; Phenotype; Principal Investigator; Process; Publishing; Reporting; Reproducibility; Research; Role; Services; Standardization; Techniques; Technology; Visualization; chromosome conformation capture; complement C4c; computational pipelines; computational platform; cost; data exchange; data integration; data management; data quality; data sharing; design; diverse data; epigenomics; genomic data; high throughput analysis; medical schools; member; single-cell RNA sequencing; tool; transcriptome sequencing; transcriptomics; tumor initiation; tumor progression; web interface; web portal

SUMMARY The overarching goal of the Computational Core is to provide robust and reproducible analysis of high- throughput genomic (WES), epigenomic (ChIP-seq, ATAC-seq, WGBS and RRBS), chromatin conformation (Hi-C and 4C) and transcriptomic (RNA-seq and single-cell RNA-seq) data using a variety of established computational workflows, methods and tools. All genomics data will be uniformly processed by HiC-bench, our recently published computational platform. The Computational Core will provide start-to-finish standardization of the analysis of sequencing datasets, rigorous data quality assessment, integration and visualization, as well as statistical expertise. The results of the bioinformatics analyses conducted in the Core will be utilized by all three Projects, using the sharable workflows of our computational platform. Finally, the bioinformatics staff will setup a web interface for the data and analyses, accessible to all members of the proposed study. This web interface will also facilitate data sharing with the broader scientific community and the public when our studies are published.

总结 计算核心的首要目标是提供高可靠性和可重复性的分析， 通量基因组（WES）、表观基因组（ChIP-seq、ATAC-seq、WGBS和RRBS）、染色质构象 (Hi-C和4C）和转录组学（RNA-seq和单细胞RNA-seq）数据， 计算工作流程、方法和工具。所有基因组学数据将由HiC-bench统一处理，我们的 最近发布的计算平台。计算核心将提供从头到尾的标准化 测序数据集的分析，严格的数据质量评估，整合和可视化，以及 作为统计专业知识。在核心中进行的生物信息学分析的结果将被所有 三个项目，使用我们的计算平台的共享工作流程。最后，生物信息学工作人员将 为数据和分析建立一个网络界面，供拟议研究的所有成员访问。此web 接口还将促进与更广泛的科学界和公众共享数据， 发表了。