Gene panel selection for targeted spatial transcriptomics.
Genome Biol
; 25(1): 35, 2024 01 25.
Article
em En
| MEDLINE
| ID: mdl-38273415
ABSTRACT
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
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Base de dados:
MEDLINE
Assunto principal:
Técnicas Genéticas
/
Perfilação da Expressão Gênica
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article