吉奥托套件:一个多尺度和无关技术的空间多omics分析生态系统
Jiaji George Chen1, Joselyn Cristina Chávez-Fuentes2, Matthew O'Brien1
1Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA.
bioRxiv : the preprint server for biology
|December 11, 2023
概括
吉奥托套件提供了一个开源的R包,用于整合各种空间omics数据. 这种工具箱能够在各种分辨率上对多原子数据集进行可扩展的分析和可视化.
科学领域:
- 空间奥米克斯 空间奥米克斯
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 空间奥米克技术绘制组织架构和基因调节的地图.
- 这些技术产生了大量的多尺度数据,这带来了整合的挑战.
- 有效地协调各种空间奥米克数据集对于生物发现至关重要.
研究的目的:
- 介绍Giotto Suite,这是一个集成的,开源的工具箱,用于空间信息数据分析.
- 为代表和整合多样化的空间空间数据提供一个技术无关的框架.
- 为空间多原子数据分析和可视化提供可扩展,灵活和端到端的解决方案.
主要方法:
- 开发了Giotto Suite,这是一个基于R的模块化软件包.
- 创建了一个技术无关的数据框架,用于空间奥米克数据.
- 集成的分子,形态,空间和注释特征信息.
- 为基因组学和空间数据科学建立了可互操作的接口.
主要成果:
- 吉奥托套件允许以任何分辨率表示和集成各种空间奥米克数据.
- 该套件为数据分析,集成和可视化提供可扩展的解决方案.
- 证明了灵活的,多规模的,多原子数据分析工作流程.
结论:
- 吉奥托套件为空间多原子数据分析提供了一个全面的生态系统.
- 开源性质和可互操作的接口促进了定制管道的开发.
- 通过集成的空间奥米克数据,促进对生物过程和疾病的更深入的机械洞察.
更多相关视频
相关概念视频
02:02Genomics
36.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.4K
01:11Genome-wide Association Studies-GWAS
13.5K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.5K
02:51Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
02:34DNA Microarrays
17.4K
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...
17.4K
03:00Next-generation Sequencing
89.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
89.0K