A unified pipeline for FISH spatial transcriptomics.
FISH
computational methods
genomics
spatial transcriptomics
transcriptomics
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
13 Sep 2023
13 Sep 2023
Historique:
received:
21
02
2023
revised:
23
06
2023
accepted:
24
07
2023
medline:
18
9
2023
pubmed:
18
9
2023
entrez:
18
9
2023
Statut:
epublish
Résumé
High-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and its effects on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for fluorescence
Identifiants
pubmed: 37719153
doi: 10.1016/j.xgen.2023.100384
pii: S2666-979X(23)00181-7
pmc: PMC10504669
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100384Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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