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geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Published version
Peer-reviewed

Change log

Authors

Missarova, Alsu 
Jain, Jaison 
Butler, Andrew 
Ghazanfar, Shila 
Stuart, Tim 

Abstract

scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.

Description

Funder: European Molecular Biology Laboratory (EMBL) (4843)

Keywords

Method

Journal Title

Genome Biol

Conference Name

Journal ISSN

1474-7596
1474-760X

Volume Title

22

Publisher

Springer Science and Business Media LLC
Sponsorship
national institutes of health (1OT2OD026673-01, 1OT2OD026673-01, RM1HG011014-02, K99HG011489-01, U54AI142766, U54AI142766, U54AI142766, U54AI142766)
royal society (gb) (NIF\R1\181950)
leona m. and harry b. helmsley charitable trust (2004-03813, 2004-03813)
cancer research uk (C9545/A29580)