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references.bib
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title = {{Scater}: pre-processing, quality control, normalization and visualization of single-cell {RNA-seq} data in {R}},
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title = {{spatialLIBD}: an {R/Bioconductor} package to visualize spatially-resolved transcriptomics data},
author = {Pardo, Brenda and Spangler, Abby and Weber, Lukas M. and Page, Stephanie C. and Hicks, Stephanie C. and Jaffe, Andrew E. and Martinowich, Keri and Maynard, Kristen R. and Collado-Torres, Leonardo},
journal = {BMC Genomics},
year = {2022},
number = {23},
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}
@article{Righelli2022,
title = {{SpatialExperiment}: infrastructure for spatially-resolved transcriptomics data in {R} using {Bioconductor}},
author = {Righelli, Dario and Weber, Lukas M. and Crowell, Helena L. and Pardo, Brenda and Collado-Torres, Leonardo and Ghazanfar, Shila and Lun, Aaron T. L. and Hicks, Stephanie C. and Risso, Davide},
journal = {Bioinformatics},
year = {2022},
volume = {38},
number = {11},
pages = {3128-3131},
url = {https://doi.org/10.1093/bioinformatics/btac299}
}
@article{Stahl2016,
title = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics},
author = {St{\aa}hl, Patrik L. and Salm{\'e}n, Fredrik and Vickovic, Sanja and Lundmark, Anna and Navarro, Jos{\'e} Fern{\'a}ndez and Magnusson, Jens and Giacomello, Stefania and Asp, Michaela and Westholm, Jakub O. and Huss, Mikael and Mollbrink, Annelie and Linnarsson, Sten and Codeluppi, Simone and Borg, {\AA}ke and Pont{\'e}n, Fredrik and Costea, Paul Igor and Sahl{\'e}n, Pelin and Mulder, Jan and Bergmann, Olaf and Lundeberg, Joakim and Fris{\'e}n, Jonas"},
journal = {Science},
year = {2016},
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number = {6294},
pages = {78-82},
url = {https://doi.org/10.1126/science.aaf2403}
}
@article{Svensson2018,
title = {{SpatialDE}: identification of spatially variable genes},
author = {Svensson, Valentine and Teichmann, Sarah A. and Stegle, Oliver},
journal = {Nature Methods},
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url = {https://doi.org/10.1038/nmeth.4636}
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@article{Sun2020,
title = {Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies},
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journal = {Nature Methods},
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url = {https://doi.org/10.1038/s41592-019-0701-7}
}
@article{Zhu2021,
title = {{SPARK-X}: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies},
author = {Zhu, Jiaqiang and Sun, Shiquan and Zhou, Xiang},
journal = {Genome Biology},
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volume = {22},
pages = {184},
url = {https://doi.org/10.1186/s13059-021-02404-0}
}
@article{Weber2023,
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},
year = {2023},
volume = {14},
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url = {https://doi.org/10.1038/s41467-023-39748-z}
}
@article{Tippani2022,
title = {{VistoSeg}: processing utilities for high-resolution {Visium/Visium-IF} images for spatial transcriptomics data},
author = {Tippani, Madhavi and Divecha, Heena R. and Catallini II, Joseph L. and Kwon, Sang Ho and Weber, Lukas M. and Spangler, Abby and Jaffe, Andrew E. and Hicks, Stephanie C. and Martinowich, Keri and Collado-Torres, Leonardo and Page, Stephanie C. and Maynard, Kristen R.},
journal = {bioRxiv},
year = {2022},
url = {https://doi.org/10.1101/2021.08.04.452489}
}
@article{Zhao2021,
title = {Spatial transcriptomics at subspot resolution with {BayesSpace}},
author = {Zhao, Edward and Stone, Matthew R. and Ren, Xing and Guenthoer, Jamie and Smythe, Kimberly S. and Pulliam, Thomas and Williams, Stephen R. and Uytingco, Cedric R. and Taylor, Sarah E. B. and Nghiem, Paul and Bielas, Jason H. and Gottardo, Raphael},
journal = {Nature Biotechnology},
year = {2021},
volume = {39},
pages = {1375-1384},
url = {https://doi.org/10.1038/s41587-021-00935-2}
}
@article{Stickels2021,
title = {Highly sensitive spatial transcriptomics at near-cellular resolution with {Slide-seqV2}},
author = {Stickels, Robert R. and Murray, Evan and Kumar, Pawan and Li, Jilong and Marshall, Jamie L. and Di Bella, Daniela J. and Arlotta, Paola and Macosko, Evan Z. and Chen, Fei},
journal = {Nature Biotechnology},
year = {2021},
volume = {39},
pages = {313-319},
url = {https://doi.org/10.1038/s41587-020-0739-1}
}
@article{Eng2019,
title = {Transcriptome-scale super-resolved imaging in tissues by {RNA} {seqFISH+}},
author = {Eng, Chee-Huat Linus and Lawson, Michael and Zhu, Qian and Dries, Ruben and Koulena, Noushin and Takei, Yodai and Yun, Jina and Cronin, Christopher and Karp, Christoph and Yuan, Guo-Cheng and Cai, Long},
journal = {Nature},
year = {2019},
volume = {568},
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}
@article{Xia2019,
title = {Spatial transcriptome profiling by {MERFISH} reveals subcellular {RNA} compartmentalization and cell cycle-dependent gene expression},
author = {Xia, Chenglong and Fan, Jean and Emanuel, George and Hao, Junjie and Zhuang, Xiaowei},
journal = {Proceedings of the National Academy of Sciences of the USA},
year = {2019},
volume = {116},
number = {39},
pages = {19490-19499},
url = {https://doi.org/10.1073/pnas.1912459116}
}
@article{Li2022,
title = {Benchmarking computational integration methods for spatial transcriptomics data},
author = {Li, Yijun and Stanojevic, Stefan and He, Bing and Jing, Zheng and Huang, Qianhui and Kang, Jian and Garmire, Lana X.},
journal = {bioRxiv},
year = {2022},
url = {https://doi.org/10.1101/2021.08.27.457741}
}
@article{Bressan2023,
title = {The dawn of spatial omics},
author = {Bressan, Dario and Battistoni, Giorgia and Hannon, Gregory J.},
journal = {Science},
year = {2023},
volume = {381},
number = {6657},
url = {https://doi.org/10.1126/science.abq4964}
}
@article{Moses2022,
title = {Museum of spatial transcriptomics},
author = {Moses, Lambda and Pachter, Lior},
journal = {Nature Methods},
year = {2022},
volume = {19},
pages = {534-546},
url = {https://doi.org/10.1038/s41592-022-01409-2}
}
@article{PetersCouto2023,
title = {{MoleculeExperiment} enables consistent infrastructure for molecule-resolved spatial transcriptomics data in {Bioconductor}},
author = {Peters Couto, Bárbara Zita and Robertson, Nicholas and Patrick, Ellis and Ghazanfar, Shila},
journal = {bioRxiv},
year = {2023},
url = {https://doi.org/10.1101/2023.05.16.541040}
}
@article{Moses2023,
title = {{Voyager}: exploratory single-cell genomics data analysis with geospatial statistics},
author = {Moses, Lambda and Einarsson, Pétur Helgi and Jackson, Kayla and Luebbert, Laura and Booeshaghi, A. Sina and Antonsson, Sindri and Bray, Nicolas and Melsted, Páll and Pachter, Lior},
journal = {bioRxiv},
year = {2023},
url = {https://doi.org/10.1101/2023.07.20.549945}
}
@article{Hu2021,
title = {{SpaGCN}: {Integrating} gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network},
author = {Hu, Jian and Li, Xiangjie and Coleman, Kyle and Schroeder, Amelia and Ma, Nan and Irwin, David J. and Lee, Edward B. and Shinohara, Russell T. and Li, Mingyao},
journal = {Nature Methods},
year = {2021},
volume = {18},
pages = {1342-1351},
url = {https://doi.org/10.1038/s41592-021-01255-8}
}
@article{Liu2023,
title = {Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with {PRECAST}},
author = {Liu, Wei and Liao, Xu and Luo, Ziye and Yang, Yi and Lau, Mai Chan and Jiao, Yuling and Shi, Xingjie and Zhai, Weiwei and Ji, Hongkai and Yeong, Joe and Liu, Jin},
journal = {Nature Communications},
year = {2023},
volume = {14},
pages = {296},
url = {https://doi.org/10.1038/s41467-023-35947-w}
}
@article{Canete2022,
title = {{spicyR}: spatial analysis of in situ cytometry data in {R}},
author = {Canete, Nicolas P. and Iyengar, Sourish S. and Ormerod, John T. and Baharlou, Heeva and Harman, Andrew N. and Patrick, Ellis},
journal = {Bioinformatics},
year = {2022},
volume = {38},
issue = {11},
pages = {3099-3105},
url = {https://doi.org/10.1093/bioinformatics/btac268}
}
@article{Singhal2024,
title = {{BANKSY} unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis},
author = {Singhal, Vipul and Chou, Nigel and Lee, Joseph and Yue, Yifei and Liu, Jinyue and Chock, Wan Kee and Lin, Li and Chang, Yun-Ching and Teo, Erica Mei Ling and Aow, Jonathan and Lee, Hwee Kuan and Chen, Kok Hao and Prabhakar, Shyam},
journal = {Nature Genetics},
year = {2024},
url = {https://doi.org/10.1038/s41588-024-01664-3}
}