Kayla C Jackson, A Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Orhan Hosten-Mittermaier, Lior Pachter
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Characterization of spatial homogeneous regions in tissues with concordex.
The rapid advancement of spatially resolved transcriptomics (SRT) technologies has facilitated exploration of how gene expression varies across tissues. However, identifying spatially variable genes remains challenging due to confounding variation introduced by the spatial distribution of cell types. We introduce a new approach to identifying spatial domains that are homogeneous with respect to cell-type composition that facilitates the decomposition of gene expression patterns by cell-type and spatial variation. Our method, called concordex, is efficient and effective across technological platforms and tissue types, and using several biological datasets we show that it can be used to identify genes with subtle variation patterns that are missed when considering only cell-type variation, or spatial variation, alone. The concordex tool is freely available at https://github.com/pachterlab/concordexR.
期刊介绍:
Science and technology related to the basic physics and engineering of magnetism, magnetic materials, applied magnetics, magnetic devices, and magnetic data storage. The IEEE Transactions on Magnetics publishes scholarly articles of archival value as well as tutorial expositions and critical reviews of classical subjects and topics of current interest.