Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
Nucleic Acids Res. 2022 Jul 5;50(W1):W427-W433. doi: 10.1093/nar/gkac322.
Here we present ICARUS, a web server to enable users without experience in R to undertake single cell RNA-seq analysis. The focal point of ICARUS is its intuitive tutorial-style user interface, designed to guide logical navigation through the multitude of pre-processing, analysis and visualization steps. ICARUS is easily accessible through a dedicated web server (https://launch.icarus-scrnaseq.cloud.edu.au/) and avoids installation of software on the user's computer. Notable features include the facility to apply quality control thresholds and adjust dimensionality reduction and cell clustering parameters. Data is visualized through 2D/3D UMAP and t-SNE plots and may be curated to remove potential confounders such as cell cycle heterogeneity. ICARUS offers flexible differential expression analysis with user-defined cell groups and gene set enrichment analysis to identify likely affected biological pathways. Eleven organisms including human, dog, mouse, rat, zebrafish, fruit fly, nematode, yeast, cattle, chicken and pig are currently supported. Visualization of multimodal data including those generated by CITE-seq and the 10X Genomics Multiome kit is included. ICARUS incorporates a function to save the current state of analysis avoiding computationally intensive steps during repeat analysis. The complete analysis of a typical single cell RNA-seq dataset by inexperienced users may be achieved in 1-2 h.
这里我们介绍了 ICARUS，这是一个网络服务器，使没有 R 经验的用户能够进行单细胞 RNA-seq 分析。ICARUS 的重点是其直观的教程式用户界面，旨在指导用户在众多预处理、分析和可视化步骤中进行逻辑导航。ICARUS 通过专用的网络服务器（https://launch.icarus-scrnaseq.cloud.edu.au/）轻松访问，避免在用户计算机上安装软件。其显著特点包括应用质量控制阈值以及调整降维和细胞聚类参数的功能。通过 2D/3D UMAP 和 t-SNE 图可视化数据，并可以通过剔除细胞周期异质性等潜在混杂因素来对数据进行编辑。ICARUS 提供了灵活的差异表达分析，用户可以定义细胞群，并进行基因集富集分析，以确定可能受影响的生物学途径。目前支持包括人类、狗、鼠、大鼠、斑马鱼、果蝇、线虫、酵母、牛、鸡和猪在内的 11 种生物。包括 CITE-seq 和 10X Genomics Multiome 试剂盒生成的多模态数据的可视化也包括在内。ICARUS 还包含了一个保存分析状态的功能，避免了在重复分析中进行计算密集型步骤。无经验用户可以在 1-2 小时内完成典型的单细胞 RNA-seq 数据集的完整分析。
