STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data.

SUMMARY STACAS is a computational method for the identification of integration anchors in the Seurat environment, optimized for the integration of single-cell (sc)RNA-seq datasets that share only a subset of cell types. We demonstrate that by i) correcting batch effects while preserving relevant biological variability across datasets, ii) filtering aberrant integration anchors with a quantitative distance measure, and iii) constructing optimal guide trees for integration, STACAS can accurately align scRNA-seq datasets composed of only partially overlapping cell populations. AVAILABILITY Source code and R package available at https://github.com/carmonalab/STACAS; Docker image available at https://hub.docker.com/repository/docker/mandrea1/stacas_demo. SUPPLEMENTARY INFORMATION Interactive TIL atlas constructed using STACAS: http://tilatlas.unil.ch.