Tutorials
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
Tutorial 6: LungMAP Ingest Broker Submission Guide
Tutorial 7: LungMAP Ingest Broker Spreadsheet Guide
Tutorial 8: scALABLE Platform for Comprehensive Omics Exploration
Video Tutorials
Videos 1 to 7 play on this page. Each one also plays from a link at the top of the page it covers.
Video 1 · 5:00 LungMAP.net - Multimodal AI Exploration of the Lung A tour of LungMAP.net: its tools, the CellRef reference atlases, and the platforms that analyze and compare multimodal data, including your own.
Video 2 · 3:01 LungMAP.net - Study View Visualize Data and the study pages: find a study by compendium, filter or name, then open its tools, downloads, samples and sample network.
Video 3 · 4:13 LungMAP.net - Molecule at a Glance Search by molecule: statistics and viewers for one gene, metabolite, lipid, surface antigen or transcription factor across the CellRef2.0 atlas.
Video 4 · 4:38 LungMAP.net - Multimodal Signature Discovery and Systems Exploration Discover: search the signature genes and statistics of CellRef2.0 in one modality or across modalities, with pathway, network, GWAS and drug analyses.
Video 5 · 3:26 LungMAP.net - CellCards CellCards: nomenclature, identifiers, descriptions, markers and images for each lung cell type, and the CellRef viewers in ShinyCell and CELLxGENE.
Video 6 · 2:03 LungMAP.net - Single-Cell Matrix Tools The Single-Cell Matrix Service: select cells of healthy and diseased lung by covariate, and download them as an h5ad file.
Video 7 · 2:00 LungMAP.net - Niche Explorer The Niche Explorer: computationally predicted spatial niches of fibrotic lung disease, and the gene expression differences between them.
Video 8 · on Vimeo scALABLE (cellHarmony-web) Submit Data: align your own single-cell data to a reference atlas, then explore it and compare groups in scALABLE.
Video 9 · on Vimeo Exploring and Analyzing LungMAP Data in Terra
Video 10 · on YouTube Data Submission and Metadata Curation in the LungMAP Ingest Broker