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

Details

Serval ID
serval:BIB_D3F01C447F08
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data.
Journal
Bioinformatics
Author(s)
Andreatta M., Carmona S.J.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
In Press
Peer-reviewed
Oui
Language
english
Notes
Publication types: Journal Article
Publication Status: aheadofprint
Abstract
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.
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.
Interactive TIL atlas constructed using STACAS: http://tilatlas.unil.ch.
Pubmed
Open Access
Yes
Funding(s)
Swiss National Science Foundation / Projects / 00P3_180010
Create date
10/09/2020 10:18
Last modification date
05/10/2020 5:26
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