伏塔：高级分子网络分析。
VOLTA: adVanced mOLecular neTwork Analysis.
机构信息
Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.
BioMediTech Institute, Tampere University, Tampere 33520, Finland.
出版信息
Bioinformatics. 2021 Dec 7;37(23):4587-4588. doi: 10.1093/bioinformatics/btab642.
MOTIVATION
Network analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines.
RESULTS
We developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a 'plug and play' system is provided.
AVAILABILITY AND IMPLEMENTATION
The package and used data are available at GitHub: https://github.com/fhaive/VOLTA and 10.5281/zenodo.5171719.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
网络分析是一种研究生物系统的强大方法。它通常被应用于研究转录组学实验中得出的基因共表达模式。尽管共表达分析被广泛应用，但仍然缺乏基于不同网络类型和分析场景（例如通过功能可访问性）开放和可定制的工具，同时也为新手用户提供完整的分析流程，使其更便于使用。
结果
我们开发了 VOLTA，这是一个适用于复杂共表达网络分析的 Python 包。VOLTA 旨在允许用户直接访问各个函数，同时也提供完整的分析流程。此外，VOLTA 在可能的情况下为每个分析步骤提供了多种算法（例如，提供了多种社区检测或聚类算法），从而使用户能够根据自己的需求进行分析。这使得 VOLTA 非常适合希望为各种网络构建自己的分析流程的经验丰富的用户，以及为提供了“即插即用”系统的新手用户。
可用性和实现
该软件包和使用的数据可在 GitHub 上获得：https://github.com/fhaive/VOLTA 和 10.5281/zenodo.5171719。
补充信息
补充数据可在生物信息学在线获得。
Zotero 插件