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@article{Virshup_2023,
doi = {10.1038/s41587-023-01733-8},
url = {https://doi.org/10.1038%2Fs41587-023-01733-8},
year = 2023,
month = {apr},
publisher = {Springer Science and Business Media {LLC}},
author = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
journal = {Nature Biotechnology}
}
@misc{Amid2019,
author = {Amid, Ehsan and Warmuth, Manfred K.},
doi = {10.48550/ARXIV.1910.00204},
url = {https://arxiv.org/abs/1910.00204},
keywords = {Machine Learning (cs.LG), Machine Learning (stat.ML), FOS: Computer and information sciences, FOS: Computer and information sciences},
title = {TriMap: Large-scale Dimensionality Reduction Using Triplets},
publisher = {arXiv},
year = {2019},
copyright = {arXiv.org perpetual, non-exclusive license},
}
@article{Amir2013,
author = {Amir, El-ad David and Davis, Kara L and Tadmor, Michelle D and Simonds, Erin F and Levine, Jacob H and Bendall, Sean C and Shenfeld, Daniel K and Krishnaswamy, Smita and Nolan, Garry P and Pe’er, Dana},
title = {viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia},
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journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
year = {2013},
month = {may},
pages = {545--552},
}
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author = {Angerer, Philipp and Haghverdi, Laleh and Büttner, Maren and Theis, Fabian J. and Marr, Carsten and Buettner, Florian},
title = {destiny: diffusion maps for large-scale single-cell data in R},
volume = {32},
issn = {1367-4803},
url = {https://doi.org/10.1093/bioinformatics/btv715},
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journal = {Bioinformatics},
publisher = {Oxford University Press (OUP)},
year = {2015},
month = {dec},
pages = {1241--1243},
}
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month = {oct},
pages = {346--360.e4},
}
@article{Becht2018,
author = {Becht, Etienne and McInnes, Leland and Healy, John and Dutertre, Charles-Antoine and Kwok, Immanuel W H and Ng, Lai Guan and Ginhoux, Florent and Newell, Evan W},
title = {Dimensionality reduction for visualizing single-cell data using UMAP},
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journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
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month = {dec},
pages = {38--44},
}
@article{Bernstein2020,
author = {Bernstein, Nicholas J. and Fong, Nicole L. and Lam, Irene and Roy, Margaret A. and Hendrickson, David G. and Kelley, David R.},
title = {Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning},
volume = {11},
issn = {2405-4712},
url = {https://doi.org/10.1016/j.cels.2020.05.010},
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journal = {Cell Systems},
publisher = {Elsevier BV},
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pages = {95--101.e5},
}
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author = {Blondel, Vincent D and Guillaume, Jean-Loup and Lambiotte, Renaud and Lefebvre, Etienne},
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publisher = {Elsevier BV},
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month = {feb},
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}
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author = {Butler, Andrew and Hoffman, Paul and Smibert, Peter and Papalexi, Efthymia and Satija, Rahul},
title = {Integrating single-cell transcriptomic data across different conditions, technologies, and species},
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month = {apr},
pages = {411--420},
}
@misc{Chippada2018,
author = {Chippada, Bhargav},
title = {ForceAtlas2 for Python},
year = {2018},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/bhargavchippada/forceatlas2},
howpublished = {\url{https://github.com/bhargavchippada/forceatlas2}},
}
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author = {Csárdi, G. and Nepusz, T.},
added-at = {2011-03-14T01:02:14.000+0100},
url = {https://www.bibsonomy.org/bibtex/252e3e774bac8424cc9a3845a9c597344/lantiq},
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year = {2006},
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@article{Eraslan2019,
author = {Eraslan, G\"{o}kcen and Simon, Lukas M. and Mircea, Maria and Mueller, Nikola S. and Theis, Fabian J.},
title = {Single-cell RNA-seq denoising using a deep count autoencoder},
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number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
year = {2019},
month = {jan},
}
@misc{Fechtner2018,
author = {Fechtner, Ron},
title = {PyPairs - A python scRNA-Seq classifier},
year = {2018},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/rfechtner/pypairs},
howpublished = {\url{https://github.com/rfechtner/pypairs}},
}
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author = {Fruchterman, Thomas M. J. and Reingold, Edward M.},
title = {Graph drawing by force‐directed placement},
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author = {Gardner, Timothy S. and Cantor, Charles R. and Collins, James J.},
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@article{Haghverdi2015,
author = {Haghverdi, Laleh and Buettner, Florian and Theis, Fabian J.},
title = {Diffusion maps for high-dimensional single-cell analysis of differentiation data},
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url = {https://doi.org/10.1093/bioinformatics/btv325},
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journal = {Bioinformatics},
publisher = {Oxford University Press (OUP)},
year = {2015},
month = {may},
pages = {2989--2998},
}
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author = {Haghverdi, Laleh and Büttner, Maren and Wolf, F Alexander and Buettner, Florian and Theis, Fabian J},
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author = {Haghverdi, Laleh and Lun, Aaron T L and Morgan, Michael D and Marioni, John C},
title = {Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors},
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author = {Hie, Brian and Bryson, Bryan and Berger, Bonnie},
title = {Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
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url = {https://doi.org/10.1038/s41587-019-0113-3},
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pages = {685--691},
}
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author = {Kang, Chris},
title = {mnnpy - MNN-correct in python},
year = {2018},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/chriscainx/mnnpy},
howpublished = {\url{https://github.com/chriscainx/mnnpy}},
}
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title = {Fast, sensitive and accurate integration of single-cell data with Harmony},
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@article{Lotfollahi2019,
author = {Lotfollahi, Mohammad and Wolf, F. Alexander and Theis, Fabian J.},
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year = {2021},
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}
@misc{McInnes2018,
author = {McInnes, Leland and Healy, John and Melville, James},
doi = {10.48550/ARXIV.1802.03426},
url = {https://arxiv.org/abs/1802.03426},
keywords = {Machine Learning (stat.ML), Computational Geometry (cs.CG), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},
title = {UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction},
publisher = {arXiv},
year = {2018},
copyright = {arXiv.org perpetual, non-exclusive license},
}
@article{Moignard2015,
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title = {Decoding the regulatory network of early blood development from single-cell gene expression measurements},
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pages = {269--276},
}
@article{Moon2019,
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title = {Visualizing structure and transitions in high-dimensional biological data},
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}
@article{Muraro2016,
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pages = {385--394.e3},
}
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}
@article{Ntranos2019,
author = {Ntranos, Vasilis and Yi, Lynn and Melsted, Páll and Pachter, Lior},
title = {A discriminative learning approach to differential expression analysis for single-cell RNA-seq},
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