references.bib

@article {Moses2025.02.24.640007,
	author = {Moses, Lambda and Huseynov, Alik and Rich, Joseph M and Pachter, Lior},
	title = {Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment},
	elocation-id = {2025.02.24.640007},
	year = {2025},
	doi = {10.1101/2025.02.24.640007},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data.SpatialFeatureExperiment can be used to store and analyze a variety of spatial -omics data types, including data from the Visium, Xenium, MERFISH, SeqFish, and Slide-seq platforms, bringing spatial operations to the SingleCellExperiment ecosystem.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2025/02/27/2025.02.24.640007},
	eprint = {https://www.biorxiv.org/content/early/2025/02/27/2025.02.24.640007.full.pdf},
	journal = {bioRxiv}
}

@article{rao2021exploring,
  title={Exploring tissue architecture using spatial transcriptomics},
  author={Rao, Anjali and Barkley, Dalia and Fran{\c{c}}a, Gustavo S and Yanai, Itai},
  journal={Nature},
  volume={596},
  number={7871},
  pages={211--220},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{emons2025harnessing,
  title={Harnessing the potential of spatial statistics for spatial omics data with pasta},
  author={Emons, Martin and Gunz, Samuel and Crowell, Helena L and Mallona, Izaskun and Kuehl, Malte and Furrer, Reinhard and Robinson, Mark D},
  journal={Nucleic Acids Research},
  volume={53},
  number={17},
  pages={gkaf870},
  year={2025},
  publisher={Oxford University Press}
}

@article{moses2023voyager,
  title={Voyager: exploratory single-cell genomics data analysis with geospatial statistics},
  author={Moses, Lambda and Einarsson, P{\'e}tur Helgi and Jackson, Kayla and Luebbert, Laura and Booeshaghi, A Sina and Antonsson, Sindri and Bray, Nicolas and Melsted, P{\'a}ll and Pachter, Lior},
  journal={BioRxiv},
  year={2023}
}

@article{anselin1995local,
  title={Local indicators of spatial association—LISA},
  author={Anselin, Luc},
  journal={Geographical analysis},
  volume={27},
  number={2},
  pages={93--115},
  year={1995},
  publisher={Wiley Online Library}
}

@incollection{anselin2019moran,
  title={The Moran scatterplot as an ESDA tool to assess local instability in spatial association},
  author={Anselin, Luc},
  booktitle={Spatial analytical perspectives on GIS},
  pages={111--126},
  year={2019},
  publisher={Routledge}
}

@article{moran1950notes,
  title={Notes on continuous stochastic phenomena},
  author={Moran, Patrick AP},
  journal={Biometrika},
  volume={37},
  number={1/2},
  pages={17--23},
  year={1950},
  publisher={JSTOR}
}

@article{yan2025svg,
  title={Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data},
  author={Yan, Guanao and Hua, Shuo Harper and Li, Jingyi Jessica},
  journal={Nature Communications},
  volume={16},
  number={1},
  pages={1141},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@article{weber2023nnsvg,
  title={nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes},
  author={Weber, Lukas M and Saha, Arkajyoti and Datta, Abhirup and Hansen, Kasper D and Hicks, Stephanie C},
  journal={Nature communications},
  volume={14},
  number={1},
  pages={4059},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{cai2024despace,
  title={DESpace: spatially variable gene detection via differential expression testing of spatial clusters},
  author={Cai, Peiying and Robinson, Mark D and Tiberi, Simone},
  journal={Bioinformatics},
  volume={40},
  number={2},
  pages={btae027},
  year={2024},
  publisher={Oxford University Press}
}

@article{aibar2017scenic,
  title={SCENIC: single-cell regulatory network inference and clustering},
  author={Aibar, Sara and Gonz{\'a}lez-Blas, Carmen Bravo and Moerman, Thomas and Huynh-Thu, V{\^a}n Anh and Imrichova, Hana and Hulselmans, Gert and Rambow, Florian and Marine, Jean-Christophe and Geurts, Pierre and Aerts, Jan and others},
  journal={Nature methods},
  volume={14},
  number={11},
  pages={1083--1086},
  year={2017},
  publisher={Nature Publishing Group US New York}
}

@article{aran2019reference,
  title={Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage},
  author={Aran, Dvir and Looney, Agnieszka P and Liu, Leqian and Wu, Esther and Fong, Valerie and Hsu, Austin and Chak, Suzanna and Naikawadi, Ram P and Wolters, Paul J and Abate, Adam R and others},
  journal={Nature immunology},
  volume={20},
  number={2},
  pages={163--172},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

@book{baddeley2016spatial,
  title={Spatial point patterns: methodology and applications with R},
  author={Baddeley, Adrian and Rubak, Ege and Turner, Rolf and others},
  volume={1},
  year={2016},
  publisher={CRC press Boca Raton}
}

@article{gunz2025analysis,
  title={Analysis of anatomical multi-cellular structures from spatial omics data using sosta},
  author={Gunz, Samuel and Crowell, Helena L and Robinson, Mark D},
  journal={bioRxiv},
  pages={2025--10},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

@article{emons2026differential,
  title={Differential co-localisation analysis of multi-sample and multi-condition experiments with spatialFDA},
  author={Emons, Martin and Scheipl, Fabian and Gunz, Samuel and Purdom, Elizabeth and Robinson, Mark D},
  journal={bioRxiv},
  pages={2026--04},
  year={2026},
  publisher={Cold Spring Harbor Laboratory}
}