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@misc{10x2018pbmc,
title = {1k PBMCs from a Healthy Donor (v3 chemistry)},
author = {{10x Genomics}},
year = {2018},
url = {https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0}
}
@misc{10x2019pbmc,
title = {5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor with a Panel of TotalSeq-B Antibodies (v3 chemistry)},
author = {{10x Genomics}},
year = {2019},
url = {https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0}
}
@article{agostinis2022newwave,
doi = {10.1093/bioinformatics/btac149},
url = {https://doi.org/10.1093/bioinformatics/btac149},
year = {2022},
month = {Mar.},
publisher = {Oxford University Press ({OUP})},
volume = {38},
number = {9},
pages = {2648--2650},
author = {Federico Agostinis and Chiara Romualdi and Gabriele Sales and Davide Risso},
editor = {Yann Ponty},
title = {NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell {RNA}-seq data},
journal = {Bioinformatics}
}
@article{agrawal2021mde,
title = {Minimum-Distortion Embedding},
author = {Akshay Agrawal and Alnur Ali and Stephen Boyd},
year = {2021},
journal = {Foundations and Trends{\textregistered} in Machine Learning},
publisher = {Now Publishers},
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pages = {211--378},
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url = {https://doi.org/10.1561/2200000090}
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title = {Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography},
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elocation-id = {786269},
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title = {Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram},
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title = {A test metric for assessing single-cell {RNA}-seq batch correction},
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@article{cabello2020singlecellsignalr,
title = {{SingleCellSignalR}: inference of intercellular networks from single-cell transcriptomics},
author = {Simon Cabello-Aguilar and M{\'{e}}lissa Alame and Fabien Kon-Sun-Tack and Caroline Fau and Matthieu Lacroix and Jacques Colinge},
year = {2020},
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@article{cable2021robust,
title = {Robust decomposition of cell type mixtures in spatial transcriptomics},
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publisher = {Springer Science and Business Media {LLC}},
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}
@misc{cannoodt2021viashfromscripts,
doi = {10.48550/ARXIV.2110.11494},
url = {https://arxiv.org/abs/2110.11494},
author = {Cannoodt, Robrecht and Cannoodt, Hendrik and Van de Kerckhove, Eric and Boschmans, Andy and De Maeyer, Dries and Verbeiren, Toni},
keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences},
title = {Viash: from scripts to pipelines},
publisher = {arXiv},
year = {2021},
copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International}
}
@article{cao2018joint,
title = {Joint profiling of chromatin accessibility and gene expression in thousands of single cells},
author = {Junyue Cao and Darren A. Cusanovich and Vijay Ramani and Delasa Aghamirzaie and Hannah A. Pliner and Andrew J. Hill and Riza M. Daza and Jose L. McFaline-Figueroa and Jonathan S. Packer and Lena Christiansen and Frank J. Steemers and Andrew C. Adey and Cole Trapnell and Jay Shendure},
year = {2018},
month = {Sept.},
journal = {Science},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {361},
number = {6409},
pages = {1380--1385},
doi = {10.1126/science.aau0730},
url = {https://doi.org/10.1126/science.aau0730}
}
@article{cao2020human,
title = {A human cell atlas of fetal gene expression},
author = {Junyue Cao and Diana R. O'Day and Hannah A. Pliner and Paul D. Kingsley and Mei Deng and Riza M. Daza and Michael A. Zager and Kimberly A. Aldinger and Ronnie Blecher-Gonen and Fan Zhang and Malte Spielmann and James Palis and Dan Doherty and Frank J. Steemers and Ian A. Glass and Cole Trapnell and Jay Shendure},
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journal = {Science},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {370},
number = {6518},
doi = {10.1126/science.aba7721},
url = {https://doi.org/10.1126/science.aba7721}
}
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doi = {10.5194/gmdd-7-1525-2014},
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title = {Root mean square error ({RMSE}) or mean absolute error ({MAE})?}
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doi = {10.1093/nar/gkab004},
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number = {7},
pages = {e42--e42},
author = {Ruben Chazarra-Gil and Stijn van~Dongen and Vladimir~Yu Kiselev and Martin Hemberg},
title = {Flexible comparison of batch correction methods for single-cell {RNA}-seq using {BatchBench}},
journal = {Nucleic Acids Research}
}
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title = {The relationship between Precision-Recall and {ROC} curves},
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}
@string{dec = {Dec.}}
@article{Demetci2020scot,
author = {Pinar Demetci and Rebecca Santorella and Bj{\"o}rn Sandstede and William Stafford Noble and Ritambhara Singh},
title = {Gromov-Wasserstein optimal transport to align single-cell multi-omics data},
elocation-id = {2020.04.28.066787},
year = {2020},
doi = {10.1101/2020.04.28.066787},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787},
eprint = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787.full.pdf},
journal = {bioRxiv}
}
@article{dimitrov2022comparison,
title = {Comparison of methods and resources for cell-cell communication inference from single-cell {RNA}-Seq data},
author = {Daniel Dimitrov and D{\'{e}}nes T\"{u}rei and Martin Garrido-Rodriguez and Paul L. Burmedi and James S. Nagai and Charlotte Boys and Ricardo O. Ramirez Flores and Hyojin Kim and Bence Szalai and Ivan G. Costa and Alberto Valdeolivas and Aur{\'{e}}lien Dugourd and Julio Saez-Rodriguez},
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journal = {Nature Communications},
publisher = {Springer Science and Business Media {LLC}},
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month = {Oct.},
publisher = {Informa {UK} Limited},
volume = {26},
number = {4},
pages = {745--766},
author = {David Donoho},
title = {50 Years of Data Science},
journal = {Journal of Computational and Graphical Statistics}
}
@article{efremova2020cellphonedb,
title = {{CellPhoneDB}: inferring cell{\textendash}cell communication from combined expression of multi-subunit ligand{\textendash}receptor complexes},
author = {Mirjana Efremova and Miquel Vento-Tormo and Sarah A. Teichmann and Roser Vento-Tormo},
year = {2020},
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