@book{baddeleySpatialPointPatterns,
  title={Spatial point patterns: methodology and applications with R},
  author={Baddeley, Adrian and Rubak, Ege and Turner, Rolf},
  year={2015},
  publisher={CRC press}
}

@article{damondMapHumanType2019,
  title = {A {{Map}} of {{Human Type}} 1 {{Diabetes Progression}} by {{Imaging Mass Cytometry}}},
  author = {Damond, Nicolas and Engler, Stefanie and Zanotelli, Vito R. T. and Schapiro, Denis and Wasserfall, Clive H. and Kusmartseva, Irina and Nick, Harry S. and Thorel, Fabrizio and Herrera, Pedro L. and Atkinson, Mark A. and Bodenmiller, Bernd},
  year = {2019},
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  journal = {Cell Metabolism},
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  pages = {755-768.e5},
  issn = {1550-4131}
}

@article{ramsayPrincipalComponentsAnalysis2005,
  title = {Principal Components Analysis for Functional Data},
  author = {Ramsay, {\relax JO} and Silverman, {\relax BW}},
  year = {2005},
  journal = {Functional data analysis},
  pages = {147--172},
  publisher = {Springer}
}


@article{scheiplFunctionalAdditiveMixed2015,
  title={Functional additive mixed models},
  author={Scheipl, Fabian and Staicu, Ana-Maria and Greven, Sonja},
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  number={2},
  pages={477--501},
  year={2015},
  publisher={Taylor \& Francis}
}

@article{scheiplGeneralizedFunctionalAdditive2016,
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  author = {Scheipl, Fabian and Gertheiss, Jan and Greven, Sonja},
  year = {2016},
  month = jan,
  journal = {Electronic Journal of Statistics},
  volume = {10},
  number = {1},
  pages = {1455--1492},
  publisher = {{Institute of Mathematical Statistics and Bernoulli Society}},
  issn = {1935-7524, 1935-7524}
}

@article{righelli2022spatialexperiment,
  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 TL and Hicks, Stephanie C and Risso, Davide},
  journal={Bioinformatics},
  volume={38},
  number={11},
  pages={3128--3131},
  year={2022},
  publisher={Oxford University Press}
}

@Article{spatstat2005,
    title = {{spatstat}: An {R} Package for Analyzing Spatial Point Patterns},
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    volume = {12},
    number = {6},
    pages = {1--42},
  }

 @Manual{refund2024,
    title = {refund: Regression with Functional Data},
    author = {Jeff Goldsmith and Fabian Scheipl and Lei Huang and Julia Wrobel and Chongzhi Di and Jonathan Gellar and Jaroslaw Harezlak and Mathew W. McLean and Bruce Swihart and Luo Xiao and Ciprian Crainiceanu and Philip T. Reiss and Erjia Cui},
    year = {2024},
    note = {R package version 0.1-35},
  }

  @book{ramsayFunctionalDataAnalysis2009,
  title = {Functional {{Data Analysis}} with {{R}} and {{MATLAB}}},
  author = {Ramsay, James and Hooker, Giles and Graves, Spencer},
  year = {2009},
  publisher = {Springer},
  address = {New York, NY}
}

@book{pebesma2023spatial,
  title={Spatial data science: With applications in R},
  author={Pebesma, Edzer and Bivand, Roger},
  year={2023},
  publisher={Chapman and Hall/CRC}
}

@article{wood2016Smoothing,
  author = {Simon N. Wood, Natalya Pya and Benjamin Säfken},
  title = {Smoothing Parameter and Model Selection for General Smooth Models},
  journal = {Journal of the American Statistical Association},
  year = {2016},
  publisher = {ASA Website}
  }

@article{ali2024graphcompass,
  title={GraphCompass: spatial metrics for differential analyses of cell organization across conditions},
  author={Ali, Mayar and Kuijs, Merel and Hediyeh-Zadeh, Soroor and Treis, Tim and Hrovatin, Karin and Palla, Giovanni and Schaar, Anna C and Theis, Fabian J},
  journal={Bioinformatics},
  year={2024}
}

@article{canete2022spicyr,
  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}
}

@article{sun2011functional,
  title={Functional boxplots},
  author={Sun, Ying and Genton, Marc G},
  journal={Journal of Computational and Graphical Statistics},
  year={2011}
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@Manual{ramsay2024fda,
    title = {fda: Functional Data Analysis},
    author = {James Ramsay},
    year = {2024},
    note = {R package version 6.2.0},
    url = {https://CRAN.R-project.org/package=fda},
  }
  
  @article{wrobel2024mxfda,
  title={mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data},
  author={Wrobel, Julia and Soupir, Alex C and Hayes, Mitchell T and Peres, Lauren C and Vu, Thao and Leroux, Andrew and Fridley, Brooke L},
  journal={Bioinformatics Advances},
  volume={4},
  number={1},
  pages={vbae155},
  year={2024},
  publisher={Oxford University Press}
}

@article{liebl2023fast,
  title={Fast and fair simultaneous confidence bands for functional parameters},
  author={Liebl, Dominik and Reimherr, Matthew},
  journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
  volume={85},
  number={3},
  pages={842--868},
  year={2023},
  publisher={Oxford University Press US}
}
