Navigating Single-Cell Datasets

Diverse complementary omics, imaging metadata and quantitative data types are provided for interactive exploration in LungMAP.net. In addition to these LungMAP hosts LungMAP consortium and community single-cell RNA-Seq datasets for humans, non-human primate and mice via a series interactive portals, spanning different time-points and disease. These websites include simple navigation as well as advanced query functions which we will walk through in the below tutorials. Advanced features include: 1) annotations of your own or community single-cell datasets with LungMAP reference cell-populations (CellCards and Azimuth), 2) identification of novel cell populations present in your dataset (healthy or diseased) (ToppGene and ToppFun) and 3) identification and visualization of differentially expressed genes at different developmental time-points or age in different lung cell populations. Website features are growing, so expect new features to be added overtime, including tutorials focusing on re-analysis of raw single-cell RNA-Seq and imaging datasets using advanced new tools (Terra.bio and OMERO, respectively).

Step-by-Step Tutorials

Tutorial 1: Supervised annotation of scRNA-Seq datasets (Azimuth)

Tutorial 2: Navigation of CellCards and Reference scRNA-Seq

Tutorial 3: Exploration of Diverse Lung scRNA-Seq Compendiums at LungMAP.net

Tutorial 4: Advanced Analysis of Lung Single-Cell Genomics Data in LGEA and ToppCell

Tutorial 5: Cloud-based omics data analysis with Terra

Video Tutorials

Video 1: LungMAP Portal Ecosystem - Understanding the Lung at the Systems Level

Video 2: Exploring and Analyzing LungMAP Data in Terra