scalign Documentation

scalign is a package for querying and mapping single cell RNA sequencing data onto a reference atlas. One may examine the spatial mapping directly onto the UMAP embeddings supplied by the atlas reference.

You should only perform basic quality control measures on raw UMI counts, filtering out cells of low quality and presumes to be doublets, and then use the UMI matrix to perform the querying step without any further integration. Since scalign will automatically read your specified batch key and correct batch effect using scVI.

Contents:

• API
  • scalign package