Please note that this application is under continual development. The latest updates were made on Feb 14, 2023

• sccmap performs connectivity map (CMAP) analysis of cell type specific transcriptional signatures generated from user-submitted scRNA-seq data.
• The input data is uploaded via two tab-delimited files:
  • “Expression data” file contains cell-level gene expression measurements.
  • “Sample data” file contains cell metadata.
• To start, you can load example data, or download example files.
  • Example files can be then uploaded to for analysis
  • Example files can also serve as templates to prepare your data for upload.
  • Uploaded data will be displayed in the Expression data and Sample information tables.
  • Data can be visualized by clicking on the Data visuals link in the header.

• After uploading data, click on Create signatures to create and analyze cell type specific transcriptional signatures.

  • Different cell types are distinguished based on the clusters variable in Sample information table.
  • A signature is created for each cluster by differential gene expression analysis between cells corresponding to different levels of the disease variable

• Click on Reset to upload new data.