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@Article{Yuhan2024,
author = {Hao, Yuhan and Stuart, Tim and Kowalski, Madeline H and Choudhary, Saket and Hoffman, Paul and Hartman, Austin and Srivastava, Avi and Molla, Gesmira and Madad, Shaista and Fernandez-Granda, Carlos and Satija, Rahul},
title = {Dictionary learning for integrative, multimodal and scalable single-cell analysis.},
journal = {Nature Biotechnology},
year = {2024},
volume = {42},
pages = {293--304},
number = {2},
doi = {10.1038/s41587-023-01767-y}
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@Book{Wickham2016,
author = {Hadley Wickham},
title = {ggplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2016},
isbn = {978-3-319-24277-4},
url = {https://ggplot2.tidyverse.org},
}

@Manual{Campitelli2025,
title = {ggnewscale: Multiple Fill and Colour Scales in 'ggplot2'},
author = {Elio Campitelli},
year = {2025},
note = {R package version 0.5.2},
url = {https://CRAN.R-project.org/package=ggnewscale},
doi = {10.32614/CRAN.package.ggnewscale},
}
  
@book{Pebesma2023,
  author = {Edzer Pebesma and Roger Bivand},
  year = 2023,
  title = {Spatial Data Science: With Applications in {R}},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton},
  URL = {https://doi.org/10.1201/9780429459016},
  doi = {10.1201/9780429459016}
}

@Article{Tercan2025,
author = {Bahar Tercan and Victor H Apolonio and Vinicius S Chagas and Christopher K Wong and others},
title = {Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods.},
journal = { STAR Protocols},
year = {2025},
volume = {6},
pages = {103681},
number = {2},
doi = {https://doi.org/10.1016/j.xpro.2025.103681}
}

@Article{Ellrott2025,
author = {Kyle Ellrott and Christopher K Wong and Christina Yau and Mauro A A Castro and others},
title = {Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.},
journal = {Cancer Cell},
year = {2025},
volume = {43},
pages = {195--212},
number = {2},
doi = {10.1016/j.ccell.2024.12.002}
}

@Article{Castro2012,
author = {Mauro AA Castro and Xin Wang and Michael NC Fletcher and Kerstin B Meyer and Florian Markowetz},
title = {RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.},
journal = {Genome Biology},
year = {2012},
volume = {13},
pages = {R29},
number = {4},
doi = {10.1186/gb-2012-13-4-r29}
}

@Article{Nepusz2006,
title = {The igraph software package for complex network research},
author = {Gabor Csardi and Tamas Nepusz},
journal = {InterJournal},
volume = {Complex Systems},
pages = {1695},
year = {2006},
url = {https://igraph.org/},
}

