eDAVE - GDC数据分析、可视化和探索工具的扩展

eDAVE - Extension of GDC data analysis, visualization, and exploration tools.

作者信息

Bińkowski Jan, Taryma-Leśniak Olga, Sokolowska Katarzyna Ewa, Przybylowicz Patrycja Kamila, Staszewski Melanie, Wojdacz Tomasz Kazimierz

机构信息

Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, Szczecin 70-204, Poland.

出版信息

Comput Struct Biotechnol J. 2023 Nov 4;21:5446-5450. doi: 10.1016/j.csbj.2023.10.057. eCollection 2023.

DOI:10.1016/j.csbj.2023.10.057

PMID:38022697

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10665591/

Abstract

Publicly available repositories such as Genomic Data Commons or Gene Expression Omnibus are a valuable research resource useful for hypothesis driven research as well as validation of the results of new experiments. Frequently however, the use of those opulent resources is challenging because advanced computational skills are required to mine deposited data. To address this challenge, we have developed eDAVE, a user-friendly, web and desktop interface enabling intuitive and robust analysis of almost 12 000 methylomes and transcriptomes from over 200 types of cells and tissues deposited in the Genomic Data Commons repository. The application is implemented in Python, supported for major browsers and available at: https://edave.pum.edu.pl/.

摘要

诸如基因组数据共享库（Genomic Data Commons）或基因表达综合数据库（Gene Expression Omnibus）等公开可用的存储库是宝贵的研究资源，对假设驱动的研究以及新实验结果的验证都很有用。然而，这些丰富资源的使用常常具有挑战性，因为挖掘已存储的数据需要先进的计算技能。为应对这一挑战，我们开发了eDAVE，这是一个用户友好的网络和桌面界面，能够对存储在基因组数据共享库中的200多种细胞和组织类型的近12000个甲基化组和转录组进行直观且可靠的分析。该应用程序用Python实现，支持主流浏览器，可通过以下网址获取：https://edave.pum.edu.pl/ 。