SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

Abstract Solid tumors are spatially heterogeneous in their genetic, molecular, and cellular composition, but recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy number alterations (CNAs), we develop Sl...

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Bibliographic Details
Main Authors: Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray, Robert Strasser, Jan Watter, Ofir Cohen, Orr Ashenberg, Daniel Abravanel, Judit Jané-Valbuena, Simon Mages, Ana Lako, Karla Helvie, Orit Rozenblatt-Rosen, Scott Rodig, Fei Chen, Nikhil Wagle, Aviv Regev, Johanna Klughammer
Format: Article
Language:English
Published: BMC 2025-05-01
Series:Genome Biology
Subjects:
Spatial transcriptomics
Slide-seq
Single-cell RNA-seq
Copy number alterations
Cancer
Tumor microenvironment
Online Access:https://doi.org/10.1186/s13059-025-03573-y
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