Getting Started with the Transcriptomics Explorer

Overview
The Transcriptomics Explorer is a browser-based tool for researchers to visualize and analyze scRNA sequencing data and related cell types for both mouse and human. A previous version of this tool - called the RNA-seq Data Navigator - is still available for both mouse and human.

Currently researchers can:

  • Explore a gene expression heatmap across cell types in the dataset, and search for genes of interest to inspect
  • Explore a tSNE or UMAP visualization of all cells in the dataset, colored by cell types or gene expression
  • Visualize a dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions
  • Find a cell type of interest in one visualization and see its characteristics in a different visualization
  • Download data files, including cell-level gene expression and taxonomic metadata and structure

Toggle Datasets
Toggle between datasets by clicking on the menu in the black bar near the top left corner of the screen. This post lists the available datasets.
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Toggle Visualizations
Toggle between the three visualizations by clicking on the “Visualizations” menu in the white bar near the top left corner of the screen.
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To get started with each visualization, see these posts:

Download Data
Several files are available for download, including cell-level gene expression, cell type taxonomy information, and cell metadata and annotations. Click “Download Data” in the bottom left part of the screen and choose the files of interest from the Download table.

Currently, the entire dataset must be downloaded as a whole.

Cell Type Nomenclature & Taxonomy
The Cell Types nomenclature is described here: Cell Type Nomenclature - brain-map.org