Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
BMC Genomics. 2019 Mar 6;20(1):177. doi: 10.1186/s12864-019-5548-x.
The use of microarrays and RNA-seq technologies is ubiquitous for transcriptome analyses in modern biology. With proper analysis tools, the differential gene expression analysis process can be significantly accelerated. Many open-source programs provide cutting-edge techniques, but these often require programming skills and lack intuitive and interactive or graphical user interfaces. To avoid bottlenecks impeding seamless analysis processing, we have developed an Interactive Gene Expression Analysis Kit, we term iGEAK, focusing on usability and interactivity. iGEAK is designed to be a simple, intuitive, light-weight that contrasts with heavy-duty programs.
iGEAK is an R/Shiny-based client-side desktop application, providing an interactive gene expression data analysis pipeline for microarray and RNA-seq data. Gene expression data can be intuitively explored using a seamless analysis pipeline consisting of sample selection, differentially expressed gene prediction, protein-protein interaction, and gene set enrichment analyses. For each analysis step, users can easily alter parameters to mine more relevant biological information.
iGEAK is the outcome of close collaboration with wet-bench biologists who are eager to easily explore, mine, and analyze new or public microarray and RNA-seq data. We designed iGEAK as a gene expression analysis pipeline tool to provide essential analysis steps and a user-friendly interactive graphical user interface. iGEAK enables users without programing knowledge to comfortably perform differential gene expression predictions and downstream analyses. iGEAK packages, manuals, tutorials, sample datasets are available at the iGEAK project homepage ( https://sites.google.com/view/iGEAK ).
微阵列和 RNA-seq 技术在现代生物学的转录组分析中被广泛应用。通过适当的分析工具，差异基因表达分析过程可以显著加快。许多开源程序提供了前沿技术，但这些程序通常需要编程技能，并且缺乏直观、交互或图形用户界面。为了避免阻碍无缝分析处理的瓶颈，我们开发了一个交互式基因表达分析工具包，我们称之为 iGEAK，专注于可用性和交互性。iGEAK 旨在成为一个简单、直观、轻量级的工具，与重型程序形成对比。
iGEAK 是一个基于 R/Shiny 的客户端桌面应用程序，为微阵列和 RNA-seq 数据提供了一个交互式基因表达数据分析管道。使用无缝分析管道，包括样本选择、差异表达基因预测、蛋白质-蛋白质相互作用和基因集富集分析，可以直观地探索基因表达数据。对于每个分析步骤，用户可以轻松更改参数，以挖掘更相关的生物学信息。
iGEAK 是与热衷于轻松探索、挖掘和分析新的或公共的微阵列和 RNA-seq 数据的湿实验生物学家密切合作的结果。我们将 iGEAK 设计为基因表达分析管道工具，提供必要的分析步骤和用户友好的交互式图形用户界面。iGEAK 使没有编程知识的用户能够舒适地进行差异基因表达预测和下游分析。iGEAK 软件包、手册、教程和示例数据集可在 iGEAK 项目主页（https://sites.google.com/view/iGEAK）上获得。
