相关实验视频

Updated: Aug 3, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

MethParquet:一种R包,用于快速高效的DNA甲基化关联分析,采用Apache Parquet

Ziqing Wang¹, Michael Cassidy¹, Danielle A Wallace^1,2,3,4

¹Department of Medicine, Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, 02215, United States.

Bioinformatics (Oxford, England)

|June 19, 2024

概括

MethParquet是一个新的R包,它使用高效的Parquet格式来加快对大型全基因组DNA甲基化数据集的分析. 这种工具减少了表观基因组广泛关联研究 (EWAS) 和甲基化风险评分计算中的计算挑战.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

全基因组DNA甲基化 (DNAm) 分析对于理解生物途径和个体表型至关重要.
从队列研究中分析大规模的DNAm数据面临着重大的计算挑战.
传统的基于行数据格式阻碍了广泛的DNAm数据集的有效存储,检索和操作.

研究的目的:

介绍MethParquet,这是第一个用于使用柱状Parquet格式进行高效DNAm数据分析的R包.
提供计算解决方案来管理和分析大型DNAm数据集.
促进DNAm研究中的标准后质量控制任务.

主要方法:

在R包中利用Apache Parquet列式存储格式.
实现数据提取,甲基化风险得分计算和全表观基因组关联研究 (EWAS) 的功能.
支持用于灵活分析的多种回归模型.

主要成果:

在大规模的EWAS中显著减少了运行时间和RAM使用量.
使用公开的甲基化数据集验证了MethParquet的效率.
建立了MethParquet作为一个高效的DNAm数据分析工具.

结论:

MethParquet有效地解决了大规模DNAm数据分析中的计算障碍.
该套件提高了EWAS中标准后质量控制任务的效率.
MethParquet为研究人员提供了一个宝贵的资源,这些研究人员使用广泛的DNA甲基化数据集.

更多相关视频

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Published on: May 20, 2018

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

相关概念视频

DNA Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

PCR - Polymerase Chain Reaction

PCR - Polymerase Chain Reaction

RACE - Rapid Amplification of cDNA Ends

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...