diff --git a/CHANGELOG.md b/CHANGELOG.md
index ac9c33a4..bdab4971 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,13 @@
- Simplify footer
- Update openproblems-v2 submodule
+* Updates to the way tasks are rendered (PR #296):
+
+ - Show task motivation, if present.
+ - Allow multiple citations for datasets, methods, and metrics.
+ - Render dataset name instead of dataset id in figures and tables.
+ - Change the way bibliographic references are rendered.
+
## BUG FIXES
* Updated the `openproblems-v2` submodule (PR #295). This fixes a deprecation error due to an update in ruamel.yaml.
diff --git a/_openproblems-v2 b/_openproblems-v2
index 6cdba417..45e9e434 160000
--- a/_openproblems-v2
+++ b/_openproblems-v2
@@ -1 +1 @@
-Subproject commit 6cdba41787f894aa4d1ff6f4b8d00d866fefb62e
+Subproject commit 45e9e434a7c99ac8beaee17af84a37d99a7e41e2
diff --git a/bibliography/library.bib b/bibliography/library.bib
index d5e34766..9c711b35 100644
--- a/bibliography/library.bib
+++ b/bibliography/library.bib
@@ -1,1070 +1,1618 @@
@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},
+ 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},
-}
+ 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},
- volume = {14},
- number = {3},
- pages = {211--378},
- doi = {10.1561/2200000090},
- url = {https://doi.org/10.1561/2200000090},
-}
+ 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},
+ volume = {14},
+ number = {3},
+ pages = {211--378},
+ doi = {10.1561/2200000090},
+ url = {https://doi.org/10.1561/2200000090}
+}
+
+
@article{aliee2021autogenes,
- title = {{AutoGeneS}: Automatic gene selection using multi-objective optimization for {RNA}-seq deconvolution},
- author = {Hananeh Aliee and Fabian J. Theis},
- year = {2021},
- month = jul,
- journal = {Cell Systems},
- publisher = {Elsevier {BV}},
- volume = {12},
- number = {7},
- pages = {706--715.e4},
- doi = {10.1016/j.cels.2021.05.006},
- url = {https://doi.org/10.1016/j.cels.2021.05.006},
-}
+ title = {{AutoGeneS}: Automatic gene selection using multi-objective optimization for {RNA}-seq deconvolution},
+ author = {Hananeh Aliee and Fabian J. Theis},
+ year = {2021},
+ month = {Jul.},
+ journal = {Cell Systems},
+ publisher = {Elsevier {BV}},
+ volume = {12},
+ number = {7},
+ pages = {706--715.e4},
+ doi = {10.1016/j.cels.2021.05.006},
+ url = {https://doi.org/10.1016/j.cels.2021.05.006}
+}
+
+
+@inproceedings{amelio2015normalized,
+ doi = {10.1145/2808797.2809344},
+ url = {https://doi.org/10.1145/2808797.2809344},
+ year = {2015},
+ month = {Aug.},
+ publisher = {{ACM}},
+ author = {Alessia Amelio and Clara Pizzuti},
+ title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?},
+ booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015}
+}
+
+
@article{andersson2020single,
- title = {Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography},
- author = {Alma Andersson and Joseph Bergenstr{\aa}hle and Michaela Asp and Ludvig Bergenstr{\aa}hle and Aleksandra Jurek and Jos{\'{e}} Fern{\'{a}}ndez Navarro and Joakim Lundeberg},
- year = {2020},
- month = oct,
- journal = {Communications Biology},
- publisher = {Springer Science and Business Media {LLC}},
- volume = {3},
- number = {1},
- doi = {10.1038/s42003-020-01247-y},
- url = {https://doi.org/10.1038/s42003-020-01247-y},
-}
+ title = {Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography},
+ author = {Alma Andersson and Joseph Bergenstr{\aa}hle and Michaela Asp and Ludvig Bergenstr{\aa}hle and Aleksandra Jurek and Jos{\'{e}} Fern{\'{a}}ndez Navarro and Joakim Lundeberg},
+ year = {2020},
+ month = {Oct.},
+ journal = {Communications Biology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {3},
+ number = {1},
+ doi = {10.1038/s42003-020-01247-y},
+ url = {https://doi.org/10.1038/s42003-020-01247-y}
+}
+
+
+@string{apr = {Apr.}}
+
+
+@string{aug = {Aug.}}
+
+
@article{batson2019molecular,
- title = {Molecular Cross-Validation for Single-Cell RNA-seq},
- author = {Batson, Joshua and Royer, Lo{\"\i}c and Webber, James},
- year = {2019},
- journal = {bioRxiv},
- publisher = {Cold Spring Harbor Laboratory},
- doi = {10.1101/786269},
- url = {https://www.biorxiv.org/content/early/2019/09/30/786269},
- elocation-id = {786269},
- eprint = {https://www.biorxiv.org/content/early/2019/09/30/786269.full.pdf},
-}
+ title = {Molecular Cross-Validation for Single-Cell RNA-seq},
+ author = {Batson, Joshua and Royer, Lo{\"\i}c and Webber, James},
+ year = {2019},
+ journal = {bioRxiv},
+ publisher = {Cold Spring Harbor Laboratory},
+ doi = {10.1101/786269},
+ url = {https://www.biorxiv.org/content/early/2019/09/30/786269},
+ elocation-id = {786269},
+ eprint = {https://www.biorxiv.org/content/early/2019/09/30/786269.full.pdf}
+}
+
+
@article{biancalani2021deep,
- title = {Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram},
- author = {Tommaso Biancalani and Gabriele Scalia and Lorenzo Buffoni and Raghav Avasthi and Ziqing Lu and Aman Sanger and Neriman Tokcan and Charles R. Vanderburg and {\AA}sa Segerstolpe and Meng Zhang and Inbal Avraham-Davidi and Sanja Vickovic and Mor Nitzan and Sai Ma and Ayshwarya Subramanian and Michal Lipinski and Jason Buenrostro and Nik Bear Brown and Duccio Fanelli and Xiaowei Zhuang and Evan Z. Macosko and Aviv Regev},
- year = {2021},
- month = oct,
- journal = {Nature Methods},
- publisher = {Springer Science and Business Media {LLC}},
- volume = {18},
- number = {11},
- pages = {1352--1362},
- doi = {10.1038/s41592-021-01264-7},
- url = {https://doi.org/10.1038/s41592-021-01264-7},
-}
+ title = {Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram},
+ author = {Tommaso Biancalani and Gabriele Scalia and Lorenzo Buffoni and Raghav Avasthi and Ziqing Lu and Aman Sanger and Neriman Tokcan and Charles R. Vanderburg and {\AA}sa Segerstolpe and Meng Zhang and Inbal Avraham-Davidi and Sanja Vickovic and Mor Nitzan and Sai Ma and Ayshwarya Subramanian and Michal Lipinski and Jason Buenrostro and Nik Bear Brown and Duccio Fanelli and Xiaowei Zhuang and Evan Z. Macosko and Aviv Regev},
+ year = {2021},
+ month = {Oct.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {18},
+ number = {11},
+ pages = {1352--1362},
+ doi = {10.1038/s41592-021-01264-7},
+ url = {https://doi.org/10.1038/s41592-021-01264-7}
+}
+
+
@article{bland2000odds,
- title = {Statistics Notes: The odds ratio},
- author = {J. M. Bland},
- year = {2000},
- month = may,
- journal = {{BMJ}},
- publisher = {{BMJ}},
- volume = {320},
- number = {7247},
- pages = {1468--1468},
- doi = {10.1136/bmj.320.7247.1468},
- url = {https://doi.org/10.1136/bmj.320.7247.1468},
-}
+ title = {Statistics Notes: The odds ratio},
+ author = {J. M. Bland},
+ year = {2000},
+ month = {May},
+ journal = {{BMJ}},
+ publisher = {{BMJ}},
+ volume = {320},
+ number = {7247},
+ pages = {1468--1468},
+ doi = {10.1136/bmj.320.7247.1468},
+ url = {https://doi.org/10.1136/bmj.320.7247.1468}
+}
+
+
+@article{breiman2001random,
+ doi = {10.1023/a:1010933404324},
+ url = {https://doi.org/10.1023/a:1010933404324},
+ year = {2001},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {45},
+ number = {1},
+ pages = {5--32},
+ author = {Leo Breiman},
+ journal = {Machine Learning}
+}
+
+
@article{bttner2018test,
- title = {A test metric for assessing single-cell {RNA}-seq batch correction},
- author = {Maren B\"{u}ttner and Zhichao Miao and F. Alexander Wolf and Sarah A. Teichmann and Fabian J. Theis},
- year = {2018},
- month = dec,
- journal = {Nature Methods},
- publisher = {Springer Science and Business Media {LLC}},
- volume = {16},
- number = {1},
- pages = {43--49},
- doi = {10.1038/s41592-018-0254-1},
- url = {https://doi.org/10.1038/s41592-018-0254-1},
-}
+ title = {A test metric for assessing single-cell {RNA}-seq batch correction},
+ author = {Maren B\"{u}ttner and Zhichao Miao and F. Alexander Wolf and Sarah A. Teichmann and Fabian J. Theis},
+ year = {2018},
+ month = {Dec.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {16},
+ number = {1},
+ pages = {43--49},
+ doi = {10.1038/s41592-018-0254-1},
+ url = {https://doi.org/10.1038/s41592-018-0254-1}
+}
+
+
@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},
- month = mar,
- journal = {Nucleic Acids Research},
- publisher = {Oxford University Press ({OUP})},
- volume = {48},
- number = {10},
- pages = {e55--e55},
- doi = {10.1093/nar/gkaa183},
- url = {https://doi.org/10.1093/nar/gkaa183},
-}
+ 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},
+ month = {Mar.},
+ journal = {Nucleic Acids Research},
+ publisher = {Oxford University Press ({OUP})},
+ volume = {48},
+ number = {10},
+ pages = {e55--e55},
+ doi = {10.1093/nar/gkaa183},
+ url = {https://doi.org/10.1093/nar/gkaa183}
+}
+
+
@article{cable2021robust,
- title = {Robust decomposition of cell type mixtures in spatial transcriptomics},
- author = {Dylan M. Cable and Evan Murray and Luli S. Zou and Aleksandrina Goeva and Evan Z. Macosko and Fei Chen and Rafael A. Irizarry},
- year = {2021},
- month = feb,
- journal = {Nature Biotechnology},
- publisher = {Springer Science and Business Media {LLC}},
- volume = {40},
- number = {4},
- pages = {517--526},
- doi = {10.1038/s41587-021-00830-w},
- url = {https://doi.org/10.1038/s41587-021-00830-w},
-}
+ title = {Robust decomposition of cell type mixtures in spatial transcriptomics},
+ author = {Dylan M. Cable and Evan Murray and Luli S. Zou and Aleksandrina Goeva and Evan Z. Macosko and Fei Chen and Rafael A. Irizarry},
+ year = {2021},
+ month = {Feb.},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {40},
+ number = {4},
+ pages = {517--526},
+ doi = {10.1038/s41587-021-00830-w},
+ url = {https://doi.org/10.1038/s41587-021-00830-w}
+}
+
+
@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}
-}
+ 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 = sep,
- 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},
-}
+ 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},
- year = {2020},
- month = nov,
- 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},
-}
+ 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},
+ year = {2020},
+ month = {Nov.},
+ 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}
+}
+
+
+@article{chai2014root,
+ doi = {10.5194/gmdd-7-1525-2014},
+ url = {https://doi.org/10.5194/gmdd-7-1525-2014},
+ year = {2014},
+ month = {Feb.},
+ publisher = {Copernicus {GmbH}},
+ author = {T. Chai and R. R. Draxler},
+ title = {Root mean square error ({RMSE}) or mean absolute error ({MAE})?}
+}
+
+
+@article{chazarragil2021flexible,
+ doi = {10.1093/nar/gkab004},
+ url = {https://doi.org/10.1093/nar/gkab004},
+ year = {2021},
+ month = {Feb.},
+ publisher = {Oxford University Press ({OUP})},
+ volume = {49},
+ 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}
+}
+
+
@article{chen2009local,
- title = {Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis},
- author = {Lisha Chen and Andreas Buja},
- year = {2009},
- month = mar,
- journal = {Journal of the American Statistical Association},
- publisher = {Informa {UK} Limited},
- volume = {104},
- number = {485},
- pages = {209--219},
- doi = {10.1198/jasa.2009.0111},
- url = {https://doi.org/10.1198/jasa.2009.0111},
-}
+ title = {Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis},
+ author = {Lisha Chen and Andreas Buja},
+ year = {2009},
+ month = {Mar.},
+ journal = {Journal of the American Statistical Association},
+ publisher = {Informa {UK} Limited},
+ volume = {104},
+ number = {485},
+ pages = {209--219},
+ doi = {10.1198/jasa.2009.0111},
+ url = {https://doi.org/10.1198/jasa.2009.0111}
+}
+
+
@inproceedings{chen2016xgboost,
- title = {{XGBoost}},
- author = {Tianqi Chen and Carlos Guestrin},
- year = {2016},
- month = aug,
- booktitle = {Proceedings of the 22nd {ACM} {SIGKDD} International Conference on Knowledge Discovery and Data Mining},
- publisher = {{Acm}},
- doi = {10.1145/2939672.2939785},
- url = {https://doi.org/10.1145/2939672.2939785},
-}
+ title = {{XGBoost}},
+ author = {Tianqi Chen and Carlos Guestrin},
+ year = {2016},
+ month = {Aug.},
+ booktitle = {Proceedings of the 22nd {ACM} {SIGKDD} International Conference on Knowledge Discovery and Data Mining},
+ publisher = {{Acm}},
+ doi = {10.1145/2939672.2939785},
+ url = {https://doi.org/10.1145/2939672.2939785}
+}
+
+
@article{cichocki2009fast,
- title = {Fast Local Algorithms for Large Scale Nonnegative Matrix and Tensor Factorizations},
- author = {Andrzej Cichocki and Anh-Huy Phan},
- year = {2009},
- journal = {{IEICE} Transactions on Fundamentals of Electronics, Communications and Computer Sciences},
- publisher = {Institute of Electronics, Information and Communications Engineers ({IEICE})},
- volume = {E92-a},
- number = {3},
- pages = {708--721},
- doi = {10.1587/transfun.e92.a.708},
- url = {https://doi.org/10.1587/transfun.e92.a.708},
-}
+ title = {Fast Local Algorithms for Large Scale Nonnegative Matrix and Tensor Factorizations},
+ author = {Andrzej Cichocki and Anh-Huy Phan},
+ year = {2009},
+ journal = {{IEICE} Transactions on Fundamentals of Electronics, Communications and Computer Sciences},
+ publisher = {Institute of Electronics, Information and Communications Engineers ({IEICE})},
+ volume = {E92-a},
+ number = {3},
+ pages = {708--721},
+ doi = {10.1587/transfun.e92.a.708},
+ url = {https://doi.org/10.1587/transfun.e92.a.708}
+}
+
+
@article{coifman2006diffusion,
- title = {Diffusion maps},
- author = {Ronald R. Coifman and St{\'{e}}phane Lafon},
- year = {2006},
- month = jul,
- journal = {Applied and Computational Harmonic Analysis},
- publisher = {Elsevier {BV}},
- volume = {21},
- number = {1},
- pages = {5--30},
- doi = {10.1016/j.acha.2006.04.006},
- url = {https://doi.org/10.1016/j.acha.2006.04.006},
-}
+ title = {Diffusion maps},
+ author = {Ronald R. Coifman and St{\'{e}}phane Lafon},
+ year = {2006},
+ month = {Jul.},
+ journal = {Applied and Computational Harmonic Analysis},
+ publisher = {Elsevier {BV}},
+ volume = {21},
+ number = {1},
+ pages = {5--30},
+ doi = {10.1016/j.acha.2006.04.006},
+ url = {https://doi.org/10.1016/j.acha.2006.04.006}
+}
+
+
@article{cover1967nearest,
- title = {Nearest neighbor pattern classification},
- author = {T. Cover and P. Hart},
- year = {1967},
- month = jan,
- journal = {{IEEE} Transactions on Information Theory},
- publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
- volume = {13},
- number = {1},
- pages = {21--27},
- doi = {10.1109/tit.1967.1053964},
- url = {https://doi.org/10.1109/tit.1967.1053964},
-}
+ title = {Nearest neighbor pattern classification},
+ author = {T. Cover and P. Hart},
+ year = {1967},
+ month = {Jan},
+ journal = {{IEEE} Transactions on Information Theory},
+ publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
+ volume = {13},
+ number = {1},
+ pages = {21--27},
+ doi = {10.1109/tit.1967.1053964},
+ url = {https://doi.org/10.1109/tit.1967.1053964}
+}
+
+
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-}
+ title = {The relationship between Precision-Recall and {ROC} curves},
+ author = {Jesse Davis and Mark Goadrich},
+ year = {2006},
+ booktitle = {Proceedings of the 23rd international conference on Machine learning - {ICML} {\textquotesingle}06},
+ publisher = {{ACM} Press},
+ doi = {10.1145/1143844.1143874},
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+}
+
+
+@string{dec = {Dec.}}
+
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+ 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}
+}
+
+
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-}
+ 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},
+ year = {2022},
+ month = {Jun.},
+ journal = {Nature Communications},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {13},
+ number = {1},
+ doi = {10.1038/s41467-022-30755-0},
+ url = {https://doi.org/10.1038/s41467-022-30755-0}
+}
+
+
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-}
+ doi = {10.1080/10618600.2017.1384734},
+ url = {https://doi.org/10.1080/10618600.2017.1384734},
+ year = {2017},
+ 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}
+}
+
+
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-}
+ 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},
+ month = {Feb.},
+ journal = {Nature Protocols},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {15},
+ number = {4},
+ pages = {1484--1506},
+ doi = {10.1038/s41596-020-0292-x},
+ url = {https://doi.org/10.1038/s41596-020-0292-x}
+}
+
+
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-}
+ title = {Single-cell {RNA}-seq denoising using a deep count autoencoder},
+ author = {G\"{o}kcen Eraslan and Lukas M. Simon and Maria Mircea and Nikola S. Mueller and Fabian J. Theis},
+ year = {2019},
+ month = {Jan},
+ journal = {Nature Communications},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {10},
+ number = {1},
+ doi = {10.1038/s41467-018-07931-2},
+ url = {https://doi.org/10.1038/s41467-018-07931-2}
+}
+
+
+@string{feb = {Feb.}}
+
+
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+ publisher = {{JSTOR}},
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+ journal = {International Statistical Review / Revue Internationale de Statistique}
+}
+
+
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-}
+ title = {Generalized procrustes analysis},
+ author = {J. C. Gower},
+ year = {1975},
+ month = {Mar.},
+ journal = {Psychometrika},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {40},
+ number = {1},
+ pages = {33--51},
+ doi = {10.1007/bf02291478},
+ url = {https://doi.org/10.1007/bf02291478}
+}
+
+
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- keywords = {Machine Learning (stat.ML), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},
-}
+ title = {Metrics for Multi-Class Classification: an Overview},
+ author = {Grandini, Margherita and Bagli, Enrico and Visani, Giorgio},
+ year = {2020},
+ journal = {arXiv},
+ publisher = {Cornell University},
+ doi = {10.48550/arxiv.2008.05756},
+ url = {https://arxiv.org/abs/2008.05756},
+ copyright = {arXiv.org perpetual, non-exclusive license},
+ keywords = {Machine Learning (stat.ML), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences}
+}
+
+
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- url = {https://doi.org/10.1038/s41588-021-00790-6},
-}
+ title = {{ArchR} is a scalable software package for integrative single-cell chromatin accessibility analysis},
+ author = {Jeffrey M. Granja and M. Ryan Corces and Sarah E. Pierce and S. Tansu Bagdatli and Hani Choudhry and Howard Y. Chang and William J. Greenleaf},
+ year = {2021},
+ month = {Feb.},
+ journal = {Nature Genetics},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {53},
+ number = {3},
+ pages = {403--411},
+ doi = {10.1038/s41588-021-00790-6},
+ url = {https://doi.org/10.1038/s41588-021-00790-6}
+}
+
+
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-}
+ title = {Validation of noise models for single-cell transcriptomics},
+ author = {Dominic Gr\"{u}n and Lennart Kester and Alexander van Oudenaarden},
+ year = {2014},
+ month = {Apr.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {11},
+ number = {6},
+ pages = {637--640},
+ doi = {10.1038/nmeth.2930},
+ url = {https://doi.org/10.1038/nmeth.2930}
+}
+
+
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-}
+ title = {Batch effects in single-cell {RNA}-sequencing data are corrected by matching mutual nearest neighbors},
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+ year = {2018},
+ month = {Apr.},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {36},
+ number = {5},
+ pages = {421--427},
+ doi = {10.1038/nbt.4091},
+ url = {https://doi.org/10.1038/nbt.4091}
+}
+
+
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-}
+ title = {The {CeNGEN} Project: The Complete Gene Expression Map of an Entire Nervous System},
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+ year = {2018},
+ month = {Aug.},
+ journal = {Neuron},
+ publisher = {Elsevier {BV}},
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+ number = {3},
+ pages = {430--433},
+ doi = {10.1016/j.neuron.2018.07.042},
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+}
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+
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-}
+ title = {Adjusting batch effects in microarray expression data using empirical Bayes methods},
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+ year = {2006},
+ month = {Apr.},
+ journal = {Biostatistics},
+ publisher = {Oxford University Press ({OUP})},
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+ number = {1},
+ pages = {118--127},
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+}
+
+
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-}
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+ author = {Yuhan Hao and Stephanie Hao and Erica Andersen-Nissen and William M. Mauck and Shiwei Zheng and Andrew Butler and Maddie J. Lee and Aaron J. Wilk and Charlotte Darby and Michael Zager and Paul Hoffman and Marlon Stoeckius and Efthymia Papalexi and Eleni P. Mimitou and Jaison Jain and Avi Srivastava and Tim Stuart and Lamar M. Fleming and Bertrand Yeung and Angela J. Rogers and Juliana M. McElrath and Catherine A. Blish and Raphael Gottardo and Peter Smibert and Rahul Satija},
+ year = {2021},
+ month = {Jun.},
+ journal = {Cell},
+ publisher = {Elsevier {BV}},
+ volume = {184},
+ number = {13},
+ pages = {3573--3587.e29},
+ doi = {10.1016/j.cell.2021.04.048},
+ url = {https://doi.org/10.1016/j.cell.2021.04.048}
+}
+
+
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-}
+ title = {Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
+ author = {Brian Hie and Bryan Bryson and Bonnie Berger},
+ year = {2019},
+ month = {May},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {37},
+ number = {6},
+ pages = {685--691},
+ doi = {10.1038/s41587-019-0113-3},
+ url = {https://doi.org/10.1038/s41587-019-0113-3}
+}
+
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-}
+ title = {Connectionist learning procedures},
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+ month = {Sept.},
+ journal = {Artificial Intelligence},
+ publisher = {Elsevier {BV}},
+ volume = {40},
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+}
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-}
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+ year = {2013},
+ publisher = {John Wiley \& Sons},
+ volume = {398}
+}
+
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-}
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-@string{aug = {Aug.}}
-@string{sep = {Sept.}}
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-@string{nov = {Nov.}}
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+ title = {{scMatch}: a single-cell gene expression profile annotation tool using reference datasets},
+ author = {Rui Hou and Elena Denisenko and Alistair R R Forrest},
+ year = {2019},
+ month = {Apr.},
+ journal = {Bioinformatics},
+ publisher = {Oxford University Press ({OUP})},
+ volume = {35},
+ number = {22},
+ pages = {4688--4695},
+ doi = {10.1093/bioinformatics/btz292},
+ url = {https://doi.org/10.1093/bioinformatics/btz292},
+ editor = {Janet Kelso}
+}
+
+
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-}
+ title = {Predicting cell-to-cell communication networks using {NATMI}},
+ author = {Rui Hou and Elena Denisenko and Huan Ting Ong and Jordan A. Ramilowski and Alistair R. R. Forrest},
+ year = {2020},
+ month = {Oct.},
+ journal = {Nature Communications},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {11},
+ number = {1},
+ doi = {10.1038/s41467-020-18873-z},
+ url = {https://doi.org/10.1038/s41467-020-18873-z}
+}
+
+
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-}
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+ author = {Wenpin Hou and Zhicheng Ji and Hongkai Ji and Stephanie C. Hicks},
+ year = {2020},
+ month = {Aug.},
+ journal = {Genome Biology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {21},
+ number = {1},
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-}
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+ author = {Vladimir Yu Kiselev and Tallulah S. Andrews and Martin Hemberg},
+ year = {2019},
+ month = {Jan},
+ journal = {Nature Reviews Genetics},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {20},
+ number = {5},
+ pages = {273--282},
+ doi = {10.1038/s41576-018-0088-9},
+ url = {https://doi.org/10.1038/s41576-018-0088-9}
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- doi = {10.1038/s41587-021-01139-4},
- url = {https://doi.org/10.1038/s41587-021-01139-4},
-}
+ title = {Cell2location maps fine-grained cell types in spatial transcriptomics},
+ author = {Vitalii Kleshchevnikov and Artem Shmatko and Emma Dann and Alexander Aivazidis and Hamish W. King and Tong Li and Rasa Elmentaite and Artem Lomakin and Veronika Kedlian and Adam Gayoso and Mika Sarkin Jain and Jun Sung Park and Lauma Ramona and Elizabeth Tuck and Anna Arutyunyan and Roser Vento-Tormo and Moritz Gerstung and Louisa James and Oliver Stegle and Omer Ali Bayraktar},
+ year = {2022},
+ month = {Jan},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {40},
+ number = {5},
+ pages = {661--671},
+ doi = {10.1038/s41587-021-01139-4},
+ url = {https://doi.org/10.1038/s41587-021-01139-4}
+}
+
+
@article{korsunsky2019fast,
- title = {Fast, sensitive and accurate integration of single-cell data with Harmony},
- author = {Ilya Korsunsky and Nghia Millard and Jean Fan and Kamil Slowikowski and Fan Zhang and Kevin Wei and Yuriy Baglaenko and Michael Brenner and Po-ru Loh and Soumya Raychaudhuri},
- year = {2019},
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- publisher = {Springer Science and Business Media {LLC}},
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- url = {https://doi.org/10.1038/s41592-019-0619-0},
-}
+ title = {Fast, sensitive and accurate integration of single-cell data with Harmony},
+ author = {Ilya Korsunsky and Nghia Millard and Jean Fan and Kamil Slowikowski and Fan Zhang and Kevin Wei and Yuriy Baglaenko and Michael Brenner and Po-ru Loh and Soumya Raychaudhuri},
+ year = {2019},
+ month = {Nov.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {16},
+ number = {12},
+ pages = {1289--1296},
+ doi = {10.1038/s41592-019-0619-0},
+ url = {https://doi.org/10.1038/s41592-019-0619-0}
+}
+
+
@article{kraemer2018dimred,
- title = {{dimRed} and {coRanking} - Unifying Dimensionality Reduction in R},
- author = {Guido Kraemer and Markus Reichstein and Miguel, D. Mahecha},
- year = {2018},
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- publisher = {The R Foundation},
- volume = {10},
- number = {1},
- pages = {342},
- doi = {10.32614/rj-2018-039},
- url = {https://doi.org/10.32614/rj-2018-039},
-}
+ title = {{dimRed} and {coRanking} - Unifying Dimensionality Reduction in R},
+ author = {Guido Kraemer and Markus Reichstein and Miguel, D. Mahecha},
+ year = {2018},
+ journal = {The R Journal},
+ publisher = {The R Foundation},
+ volume = {10},
+ number = {1},
+ pages = {342},
+ doi = {10.32614/rj-2018-039},
+ url = {https://doi.org/10.32614/rj-2018-039}
+}
+
+
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- url = {https://doi.org/10.1007/bf02289565},
-}
+ title = {Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis},
+ author = {J. B. Kruskal},
+ year = {1964},
+ month = {Mar.},
+ journal = {Psychometrika},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {29},
+ number = {1},
+ pages = {1--27},
+ doi = {10.1007/bf02289565},
+ url = {https://doi.org/10.1007/bf02289565}
+}
+
+
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-}
+ title = {Multimodal single cell data integration challenge: results and lessons learned},
+ author = {Lance, Christopher and Luecken, Malte D. and Burkhardt, Daniel B. and Cannoodt, Robrecht and Rautenstrauch, Pia and Laddach, Anna and Ubingazhibov, Aidyn and Cao, Zhi-Jie and Deng, Kaiwen and Khan, Sumeer and Liu, Qiao and Russkikh, Nikolay and Ryazantsev, Gleb and Ohler, Uwe and , and Pisco, Angela Oliveira and Bloom, Jonathan and Krishnaswamy, Smita and Theis, Fabian J.},
+ year = {2022},
+ journal = {bioRxiv},
+ publisher = {Cold Spring Harbor Laboratory},
+ doi = {10.1101/2022.04.11.487796},
+ url = {https://www.biorxiv.org/content/early/2022/04/12/2022.04.11.487796},
+ elocation-id = {2022.04.11.487796},
+ eprint = {https://www.biorxiv.org/content/early/2022/04/12/2022.04.11.487796.full.pdf}
+}
+
+
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- publisher = {Society for Industrial and Applied Mathematics},
- doi = {10.1137/1.9781611971217},
- url = {https://doi.org/10.1137/1.9781611971217},
-}
+ title = {Solving Least Squares Problems},
+ author = {Charles L. Lawson and Richard J. Hanson},
+ year = {1995},
+ month = {Jan},
+ publisher = {Society for Industrial and Applied Mathematics},
+ doi = {10.1137/1.9781611971217},
+ url = {https://doi.org/10.1137/1.9781611971217}
+}
+
+
@article{lee2009quality,
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- url = {https://doi.org/10.1016/j.neucom.2008.12.017},
-}
+ title = {Quality assessment of dimensionality reduction: Rank-based criteria},
+ author = {John A. Lee and Michel Verleysen},
+ year = {2009},
+ month = {Mar.},
+ journal = {Neurocomputing},
+ publisher = {Elsevier {BV}},
+ volume = {72},
+ number = {7-9},
+ pages = {1431--1443},
+ doi = {10.1016/j.neucom.2008.12.017},
+ url = {https://doi.org/10.1016/j.neucom.2008.12.017}
+}
+
+
@article{linderman2018zero,
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- year = {2018},
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- publisher = {Cold Spring Harbor Laboratory},
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- elocation-id = {397588},
- eprint = {https://www.biorxiv.org/content/early/2018/08/22/397588.full.pdf},
-}
+ title = {Zero-preserving imputation of scRNA-seq data using low-rank approximation},
+ author = {Linderman, George C. and Zhao, Jun and Kluger, Yuval},
+ year = {2018},
+ journal = {bioRxiv},
+ publisher = {Cold Spring Harbor Laboratory},
+ doi = {10.1101/397588},
+ url = {https://www.biorxiv.org/content/early/2018/08/22/397588},
+ elocation-id = {397588},
+ eprint = {https://www.biorxiv.org/content/early/2018/08/22/397588.full.pdf}
+}
+
+
@article{lopez2018deep,
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- url = {https://doi.org/10.1038/s41592-018-0229-2},
-}
+ title = {Deep generative modeling for single-cell transcriptomics},
+ author = {Romain Lopez and Jeffrey Regier and Michael B. Cole and Michael I. Jordan and Nir Yosef},
+ year = {2018},
+ month = {Nov.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {15},
+ number = {12},
+ pages = {1053--1058},
+ doi = {10.1038/s41592-018-0229-2},
+ url = {https://doi.org/10.1038/s41592-018-0229-2}
+}
+
+
@article{lopez2022destvi,
- title = {{DestVI} identifies continuums of cell types in spatial transcriptomics data},
- author = {Romain Lopez and Baoguo Li and Hadas Keren-Shaul and Pierre Boyeau and Merav Kedmi and David Pilzer and Adam Jelinski and Ido Yofe and Eyal David and Allon Wagner and Can Ergen and Yoseph Addadi and Ofra Golani and Franca Ronchese and Michael I. Jordan and Ido Amit and Nir Yosef},
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- publisher = {Springer Science and Business Media {LLC}},
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- doi = {10.1038/s41587-022-01272-8},
- url = {https://doi.org/10.1038/s41587-022-01272-8},
-}
+ title = {{DestVI} identifies continuums of cell types in spatial transcriptomics data},
+ author = {Romain Lopez and Baoguo Li and Hadas Keren-Shaul and Pierre Boyeau and Merav Kedmi and David Pilzer and Adam Jelinski and Ido Yofe and Eyal David and Allon Wagner and Can Ergen and Yoseph Addadi and Ofra Golani and Franca Ronchese and Michael I. Jordan and Ido Amit and Nir Yosef},
+ year = {2022},
+ month = {Apr.},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {40},
+ number = {9},
+ pages = {1360--1369},
+ doi = {10.1038/s41587-022-01272-8},
+ url = {https://doi.org/10.1038/s41587-022-01272-8}
+}
+
+
@article{lotfollahi2020query,
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- elocation-id = {2020.07.16.205997},
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-}
+ title = {Query to reference single-cell integration with transfer learning},
+ author = {Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D. and Khajavi, Matin and B{\"u}ttner, Maren and Avsec, Ziga and Misharin, Alexander V. and Theis, Fabian J.},
+ year = {2020},
+ journal = {bioRxiv},
+ publisher = {Cold Spring Harbor Laboratory},
+ doi = {10.1101/2020.07.16.205997},
+ url = {https://doi.org/10.1101/2020.07.16.205997},
+ elocation-id = {2020.07.16.205997},
+ eprint = {https://www.biorxiv.org/content/early/2020/07/16/2020.07.16.205997.full.pdf}
+}
+
+
@article{luecken2022benchmarking,
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- url = {https://doi.org/10.1038/s41592-021-01336-8},
-}
+ title = {Benchmarking atlas-level data integration in single-cell genomics},
+ author = {Malte D. Luecken and M. B\"{u}ttner and K. Chaichoompu and A. Danese and M. Interlandi and M. F. Mueller and D. C. Strobl and L. Zappia and M. Dugas and M. Colom{\'{e}}-Tatch{\'{e}} and Fabian J. Theis},
+ year = {2021},
+ month = {Dec.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {19},
+ number = {1},
+ pages = {41--50},
+ doi = {10.1038/s41592-021-01336-8},
+ url = {https://doi.org/10.1038/s41592-021-01336-8}
+}
+
+
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- keywords = {Machine Learning (cs.LG), Information Retrieval (cs.IR), FOS: Computer and information sciences, FOS: Computer and information sciences},
-}
+ title = {How to Evaluate Dimensionality Reduction? - Improving the Co-ranking Matrix},
+ author = {Lueks, Wouter and Mokbel, Bassam and Biehl, Michael and Hammer, Barbara},
+ year = {2011},
+ journal = {arXiv},
+ doi = {10.48550/ARXIV.1110.3917},
+ url = {https://arxiv.org/abs/1110.3917},
+ copyright = {arXiv.org perpetual, non-exclusive license},
+ keywords = {Machine Learning (cs.LG), Information Retrieval (cs.IR), FOS: Computer and information sciences, FOS: Computer and information sciences}
+}
+
+
@misc{lun2019fastmnn,
- title = {A description of the theory behind the fastMNN algorithm},
- author = {Lun, Aaron},
- year = {2019},
- url = {https://marionilab.github.io/FurtherMNN2018/theory/description.html},
+ title = {A description of the theory behind the fastMNN algorithm},
+ author = {Lun, Aaron},
+ year = {2019},
+ url = {https://marionilab.github.io/FurtherMNN2018/theory/description.html}
}
+
+
+@string{mar = {Mar.}}
+
+
+@string{may = {May}}
+
+
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- url = {https://arxiv.org/abs/1802.03426},
- copyright = {arXiv.org perpetual, non-exclusive license},
- 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},
+ author = {McInnes, Leland and Healy, John and Melville, James},
+ year = {2018},
+ journal = {arXiv},
+ publisher = {Cornell University},
+ doi = {10.48550/arxiv.1802.03426},
+ url = {https://arxiv.org/abs/1802.03426},
+ copyright = {arXiv.org perpetual, non-exclusive license},
+ keywords = {Machine Learning (stat.ML), Computational Geometry (cs.CG), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences}
+}
+
+
+@article{mereu2020benchmarking,
+ doi = {10.1038/s41587-020-0469-4},
+ author = {Mereu, Elisabetta and Lafzi, Atefeh and Moutinho, Catia and Ziegenhain, Christoph and McCarthy, Davis J and Alvarez-Varela, Adrian and Batlle, Eduard and Sagar and Gruen, Dominic and Lau, Julia K and others},
+ journal = {Nature biotechnology},
+ number = {6},
+ pages = {747--755},
+ publisher = {Nature Publishing Group US New York},
+ title = {Benchmarking single-cell {RNA}-sequencing protocols for cell atlas projects},
+ volume = {38},
+ year = {2020}
+}
+
+
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- chapter = {{R-Squared}, Adjusted {R-Squared}},
-}
+ title = {Encyclopedia of Statistics in Behavioral Science},
+ author = {Jeremy Miles},
+ year = {2005},
+ month = {Oct.},
+ publisher = {John Wiley {\&} Sons, Ltd},
+ doi = {10.1002/0470013192.bsa526},
+ url = {https://doi.org/10.1002/0470013192.bsa526},
+ chapter = {{R-Squared}, Adjusted {R-Squared}}
+}
+
+
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-}
+ title = {Visualizing structure and transitions in high-dimensional biological data},
+ author = {Kevin R. Moon and David van Dijk and Zheng Wang and Scott Gigante and Daniel B. Burkhardt and William S. Chen and Kristina Yim and Antonia van den Elzen and Matthew J. Hirn and Ronald R. Coifman and Natalia B. Ivanova and Guy Wolf and Smita Krishnaswamy},
+ year = {2019},
+ month = {Dec.},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {37},
+ number = {12},
+ pages = {1482--1492},
+ doi = {10.1038/s41587-019-0336-3},
+ url = {https://doi.org/10.1038/s41587-019-0336-3}
+}
+
+
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-}
+ title = {Assessing single-cell transcriptomic variability through density-preserving data visualization},
+ author = {Ashwin Narayan and Bonnie Berger and Hyunghoon Cho},
+ year = {2021},
+ month = {Jan},
+ journal = {Nature Biotechnology},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {39},
+ number = {6},
+ pages = {765--774},
+ doi = {10.1038/s41587-020-00801-7},
+ url = {https://doi.org/10.1038/s41587-020-00801-7}
+}
+
+
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-}
+ title = {A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation},
+ author = {Sonia Nestorowa and Fiona K. Hamey and Blanca Pijuan Sala and Evangelia Diamanti and Mairi Shepherd and Elisa Laurenti and Nicola K. Wilson and David G. Kent and Berthold G\"{o}ttgens},
+ year = {2016},
+ month = {Aug.},
+ journal = {Blood},
+ publisher = {American Society of Hematology},
+ volume = {128},
+ number = {8},
+ pages = {e20--e31},
+ doi = {10.1182/blood-2016-05-716480},
+ url = {https://doi.org/10.1182/blood-2016-05-716480}
+}
+
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+ author = {Luecken, Malte and Burkhardt, Daniel and Cannoodt, Robrecht and Lance, Christopher and Agrawal, Aditi and Aliee, Hananeh and Chen, Ann and Deconinck, Louise and Detweiler, Angela and Granados, Alejandro and Huynh, Shelly and Isacco, Laura and Kim, Yang and Klein, Dominik and DE KUMAR, BONY and Kuppasani, Sunil and Lickert, Heiko and McGeever, Aaron and Melgarejo, Joaquin and Mekonen, Honey and Morri, Maurizio and M\"{u}ller, Michaela and Neff, Norma and Paul, Sheryl and Rieck, Bastian and Schneider, Kaylie and Steelman, Scott and Sterr, Michael and Treacy, Daniel and Tong, Alexander and Villani, Alexandra-Chloe and Wang, Guilin and Yan, Jia and Zhang, Ce and Pisco, Angela and Krishnaswamy, Smita and Theis, Fabian and Bloom, Jonathan M},
+ booktitle = {Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks},
+ editor = {J. Vanschoren and S. Yeung},
+ pages = {},
+ publisher = {Curran},
+ title = {A sandbox for prediction and integration of DNA, RNA, and proteins in single cells},
+ url = {https://datasets-benchmarks-proceedings.neurips.cc/paper_files/paper/2021/file/158f3069a435b314a80bdcb024f8e422-Paper-round2.pdf},
+ volume = {1},
+ year = {2021}
+}
+
+
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+
+
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+
+
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-}
+ title = {Single-cell analysis of mixed-lineage states leading to a binary cell fate choice},
+ author = {Andre Olsson and Meenakshi Venkatasubramanian and Viren K. Chaudhri and Bruce J. Aronow and Nathan Salomonis and Harinder Singh and H. Leighton Grimes},
+ year = {2016},
+ month = {Aug.},
+ journal = {Nature},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {537},
+ number = {7622},
+ pages = {698--702},
+ doi = {10.1038/nature19348},
+ url = {https://doi.org/10.1038/nature19348}
+}
+
+
@misc{openproblems,
- title = {Open Problems},
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- year = {2022},
- url = {https://openproblems.bio},
-}
+ title = {Open Problems},
+ author = {{Open Problems for Single Cell Analysis Consortium}},
+ year = {2022},
+ url = {https://openproblems.bio}
+}
+
+
+@article{pearson1895regression,
+ doi = {10.1098/rspl.1895.0041},
+ title = {VII. Note on regression and inheritance in the case of two parents},
+ author = {Pearson, Karl},
+ journal = {proceedings of the royal society of London},
+ volume = {58},
+ number = {347-352},
+ pages = {240--242},
+ year = {1895},
+ publisher = {The Royal Society London}
+}
+
+
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-}
+ title = {On lines and planes of closest fit to systems of points in space},
+ author = {Karl Pearson},
+ year = {1901},
+ month = {Nov.},
+ journal = {The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
+ publisher = {Informa {UK} Limited},
+ volume = {2},
+ number = {11},
+ pages = {559--572},
+ doi = {10.1080/14786440109462720},
+ url = {https://doi.org/10.1080/14786440109462720}
+}
+
+
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- publisher = {Springer Science and Business Media {LLC}},
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- url = {https://doi.org/10.1038/s41592-019-0535-3},
-}
+ title = {Supervised classification enables rapid annotation of cell atlases},
+ author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
+ year = {2019},
+ month = {Sept.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {16},
+ number = {10},
+ pages = {983--986},
+ doi = {10.1038/s41592-019-0535-3},
+ url = {https://doi.org/10.1038/s41592-019-0535-3}
+}
+
+
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- doi = {10.1093/bioinformatics/btz625},
- url = {https://doi.org/10.1093/bioinformatics/btz625},
- editor = {Bonnie Berger},
-}
+ title = {{BBKNN}: fast batch alignment of single cell transcriptomes},
+ author = {Krzysztof Pola{\'{n}}ski and Matthew D Young and Zhichao Miao and Kerstin B Meyer and Sarah A Teichmann and Jong-Eun Park},
+ year = {2019},
+ month = {Aug.},
+ journal = {Bioinformatics},
+ publisher = {Oxford University Press ({OUP})},
+ doi = {10.1093/bioinformatics/btz625},
+ url = {https://doi.org/10.1093/bioinformatics/btz625},
+ editor = {Bonnie Berger}
+}
+
+
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- title = {Computation and visualization of cell{\textendash}cell signaling topologies in single-cell systems data using Connectome},
- author = {Micha Sam Brickman Raredon and Junchen Yang and James Garritano and Meng Wang and Dan Kushnir and Jonas Christian Schupp and Taylor S. Adams and Allison M. Greaney and Katherine L. Leiby and Naftali Kaminski and Yuval Kluger and Andre Levchenko and Laura E. Niklason},
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- publisher = {Springer Science and Business Media {LLC}},
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- doi = {10.1038/s41598-022-07959-x},
- url = {https://doi.org/10.1038/s41598-022-07959-x},
-}
+ title = {Computation and visualization of cell{\textendash}cell signaling topologies in single-cell systems data using Connectome},
+ author = {Micha Sam Brickman Raredon and Junchen Yang and James Garritano and Meng Wang and Dan Kushnir and Jonas Christian Schupp and Taylor S. Adams and Allison M. Greaney and Katherine L. Leiby and Naftali Kaminski and Yuval Kluger and Andre Levchenko and Laura E. Niklason},
+ year = {2022},
+ month = {Mar.},
+ journal = {Scientific Reports},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {12},
+ number = {1},
+ doi = {10.1038/s41598-022-07959-x},
+ url = {https://doi.org/10.1038/s41598-022-07959-x}
+}
+
+
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- publisher = {American Association for the Advancement of Science ({AAAS})},
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- pages = {1463--1467},
- doi = {10.1126/science.aaw1219},
- url = {https://doi.org/10.1126/science.aaw1219},
-}
+ title = {Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution},
+ author = {Samuel G. Rodriques and Robert R. Stickels and Aleksandrina Goeva and Carly A. Martin and Evan Murray and Charles R. Vanderburg and Joshua Welch and Linlin M. Chen and Fei Chen and Evan Z. Macosko},
+ year = {2019},
+ month = {Mar.},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science ({AAAS})},
+ volume = {363},
+ number = {6434},
+ pages = {1463--1467},
+ doi = {10.1126/science.aaw1219},
+ url = {https://doi.org/10.1126/science.aaw1219}
+}
+
+
@article{sarkar2021separating,
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- publisher = {Springer Science and Business Media {LLC}},
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- doi = {10.1038/s41588-021-00873-4},
- url = {https://doi.org/10.1038/s41588-021-00873-4},
-}
+ title = {Separating measurement and expression models clarifies confusion in single-cell {RNA} sequencing analysis},
+ author = {Abhishek Sarkar and Matthew Stephens},
+ year = {2021},
+ month = {May},
+ journal = {Nature Genetics},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {53},
+ number = {6},
+ pages = {770--777},
+ doi = {10.1038/s41588-021-00873-4},
+ url = {https://doi.org/10.1038/s41588-021-00873-4}
+}
+
+
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- month = may,
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- doi = {10.1213/ane.0000000000002864},
- url = {https://doi.org/10.1213/ane.0000000000002864},
-}
+ title = {Correlation Coefficients},
+ author = {Patrick Schober and Christa Boer and Lothar A. Schwarte},
+ year = {2018},
+ month = {May},
+ journal = {Anesthesia {\&} Analgesia},
+ publisher = {Ovid Technologies (Wolters Kluwer Health)},
+ volume = {126},
+ number = {5},
+ pages = {1763--1768},
+ doi = {10.1213/ane.0000000000002864},
+ url = {https://doi.org/10.1213/ane.0000000000002864}
+}
+
+
+@string{sep = {Sept.}}
+
+
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- year = {2020},
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- doi = {10.1137/1.9781611976236.36},
- url = {https://doi.org/10.1137/1.9781611976236.36},
-}
+ title = {Harmonic Alignment},
+ author = {Jay S. Stanley and Scott Gigante and Guy Wolf and Smita Krishnaswamy},
+ year = {2020},
+ month = {Jan},
+ booktitle = {Proceedings of the 2020 {SIAM} International Conference on Data Mining},
+ publisher = {Society for Industrial and Applied Mathematics},
+ pages = {316--324},
+ doi = {10.1137/1.9781611976236.36},
+ url = {https://doi.org/10.1137/1.9781611976236.36}
+}
+
+
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-}
+ title = {Simultaneous epitope and transcriptome measurement in single cells},
+ author = {Marlon Stoeckius and Christoph Hafemeister and William Stephenson and Brian Houck-Loomis and Pratip K Chattopadhyay and Harold Swerdlow and Rahul Satija and Peter Smibert},
+ year = {2017},
+ month = {Jul.},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {14},
+ number = {9},
+ pages = {865--868},
+ doi = {10.1038/nmeth.4380},
+ url = {https://doi.org/10.1038/nmeth.4380}
+}
+
+
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- journal = {Cell},
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- doi = {10.1016/j.cell.2019.05.031},
-}
+ title = {Comprehensive Integration of Single-Cell Data},
+ author = {Stuart, T. and Butler, A. and Hoffman, P. and Hafemeister, C. and Papalexi, E. and Mauck, W.M. and Hao, Y. and Stoeckius, M. and Smibert, P. and Satija, R.},
+ year = {2019},
+ journal = {Cell},
+ volume = {177},
+ number = {7},
+ pages = {1888--1902.e21},
+ doi = {10.1016/j.cell.2019.05.031}
+}
+
+
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- url = {https://doi.org/10.1038/s41598-019-45301-0},
-}
+ title = {Structure-preserving visualisation of high dimensional single-cell datasets},
+ author = {Benjamin Szubert and Jennifer E. Cole and Claudia Monaco and Ignat Drozdov},
+ year = {2019},
+ month = {Jun.},
+ journal = {Scientific Reports},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {9},
+ number = {1},
+ doi = {10.1038/s41598-019-45301-0},
+ url = {https://doi.org/10.1038/s41598-019-45301-0}
+}
+
+
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- title = {Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris},
- author = {{Tabula Muris Consortium}},
- year = {2018},
- month = oct,
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- url = {https://doi.org/10.1038/s41586-018-0590-4},
-}
+ title = {Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris},
+ author = {{Tabula Muris Consortium}},
+ year = {2018},
+ month = {Oct.},
+ journal = {Nature},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {562},
+ number = {7727},
+ pages = {367--372},
+ doi = {10.1038/s41586-018-0590-4},
+ url = {https://doi.org/10.1038/s41586-018-0590-4}
+}
+
+
@article{tabula2020single,
- title = {A single-cell transcriptomic atlas characterizes ageing tissues in the mouse},
- author = {{Tabula Muris Consortium}},
- year = {2020},
- month = jul,
- journal = {Nature},
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- url = {https://doi.org/10.1038/s41586-020-2496-1},
-}
+ title = {A single-cell transcriptomic atlas characterizes ageing tissues in the mouse},
+ author = {{Tabula Muris Consortium}},
+ year = {2020},
+ month = {Jul.},
+ journal = {Nature},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {583},
+ number = {7817},
+ pages = {590--595},
+ doi = {10.1038/s41586-020-2496-1},
+ url = {https://doi.org/10.1038/s41586-020-2496-1}
+}
+
+
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-}
+ title = {Adult mouse cortical cell taxonomy revealed by single cell transcriptomics},
+ author = {Bosiljka Tasic and Vilas Menon and Thuc Nghi Nguyen and Tae Kyung Kim and Tim Jarsky and Zizhen Yao and Boaz Levi and Lucas T Gray and Staci A Sorensen and Tim Dolbeare and Darren Bertagnolli and Jeff Goldy and Nadiya Shapovalova and Sheana Parry and Changkyu Lee and Kimberly Smith and Amy Bernard and Linda Madisen and Susan M Sunkin and Michael Hawrylycz and Christof Koch and Hongkui Zeng},
+ year = {2016},
+ month = {Jan},
+ journal = {Nature Neuroscience},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {19},
+ number = {2},
+ pages = {335--346},
+ doi = {10.1038/nn.4216},
+ url = {https://doi.org/10.1038/nn.4216}
+}
+
+
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- url = {https://doi.org/10.1038/s41592-019-0425-8},
-}
+ title = {Benchmarking single cell {RNA}-sequencing analysis pipelines using mixture control experiments},
+ author = {Luyi Tian and Xueyi Dong and Saskia Freytag and Kim-Anh L{\^{e}} Cao and Shian Su and Abolfazl JalalAbadi and Daniela Amann-Zalcenstein and Tom S. Weber and Azadeh Seidi and Jafar S. Jabbari and Shalin H. Naik and Matthew E. Ritchie},
+ year = {2019},
+ month = {May},
+ journal = {Nature Methods},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {16},
+ number = {6},
+ pages = {479--487},
+ doi = {10.1038/s41592-019-0425-8},
+ url = {https://doi.org/10.1038/s41592-019-0425-8}
+}
+
+
+@article{tran2020benchmark,
+ doi = {10.1186/s13059-019-1850-9},
+ url = {https://doi.org/10.1186/s13059-019-1850-9},
+ year = {2020},
+ month = {Jan},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {21},
+ number = {1},
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+ title = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data},
+ journal = {Genome Biology}
+}
+
+
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-}
+ title = {Recovering Gene Interactions from Single-Cell Data Using Data Diffusion},
+ author = {David van Dijk and Roshan Sharma and Juozas Nainys and Kristina Yim and Pooja Kathail and Ambrose J. Carr and Cassandra Burdziak and Kevin R. Moon and Christine L. Chaffer and Diwakar Pattabiraman and Brian Bierie and Linas Mazutis and Guy Wolf and Smita Krishnaswamy and Dana Pe'er},
+ year = {2018},
+ month = {Jul.},
+ journal = {Cell},
+ publisher = {Elsevier {BV}},
+ volume = {174},
+ number = {3},
+ pages = {716--729.e27},
+ doi = {10.1016/j.cell.2018.05.061},
+ url = {https://doi.org/10.1016/j.cell.2018.05.061}
+}
+
+
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-}
+ title = {Visualizing Data using t-SNE},
+ author = {{van der} Maaten, Laurens and Hinton, Geoffrey},
+ year = {2008},
+ journal = {Journal of Machine Learning Research},
+ volume = {9},
+ number = {86},
+ pages = {2579--2605},
+ url = {http://jmlr.org/papers/v9/vandermaaten08a.html}
+}
+
+
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-}
+ title = {Neighborhood Preservation in Nonlinear Projection Methods: An Experimental Study},
+ author = {Jarkko Venna and Samuel Kaski},
+ year = {2001},
+ booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2001},
+ publisher = {Springer Berlin Heidelberg},
+ pages = {485--491},
+ doi = {{10.1007/3-540-44668-0\_68}},
+ url = {{https://doi.org/10.1007/3-540-44668-0\_68}}
+}
+
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-}
+ title = {Local multidimensional scaling},
+ author = {Jarkko Venna and Samuel Kaski},
+ year = {2006},
+ month = {Jul.},
+ journal = {Neural Networks},
+ publisher = {Elsevier {BV}},
+ volume = {19},
+ number = {6-7},
+ pages = {889--899},
+ doi = {10.1016/j.neunet.2006.05.014},
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+}
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+ url = {https://doi.org/10.1101/2021.12.16.473007},
+ year = {2021},
+ month = {Dec.},
+ publisher = {Cold Spring Harbor Laboratory},
+ author = {Isaac Virshup and Sergei Rybakov and Fabian J. Theis and Philipp Angerer and F. Alexander Wolf},
+ title = {anndata: Annotated data}
+}
+
+
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-}
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+ author = {Wagner, Florian and Yan, Yun and Yanai, Itai},
+ year = {2018},
+ journal = {bioRxiv},
+ publisher = {Cold Spring Harbor Laboratory},
+ doi = {10.1101/217737},
+ url = {https://www.biorxiv.org/content/early/2018/04/09/217737},
+ elocation-id = {217737},
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+}
+
+
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-}
+ title = {Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo},
+ author = {Daniel E. Wagner and Caleb Weinreb and Zach M. Collins and James A. Briggs and Sean G. Megason and Allon M. Klein},
+ year = {2018},
+ month = {Jun.},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science ({AAAS})},
+ volume = {360},
+ number = {6392},
+ pages = {981--987},
+ doi = {10.1126/science.aar4362},
+ url = {https://doi.org/10.1126/science.aar4362}
+}
+
+
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-}
+ title = {Target analysis by integration of transcriptome and {ChIP}-seq data with {BETA}},
+ author = {Su Wang and Hanfei Sun and Jian Ma and Chongzhi Zang and Chenfei Wang and Juan Wang and Qianzi Tang and Clifford A Meyer and Yong Zhang and X Shirley Liu},
+ year = {2013},
+ month = {Nov.},
+ journal = {Nature Protocols},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {8},
+ number = {12},
+ pages = {2502--2515},
+ doi = {10.1038/nprot.2013.150},
+ url = {https://doi.org/10.1038/nprot.2013.150}
+}
+
+
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+ title = {Visualization and analysis of single-cell {RNA}-seq data by kernel-based similarity learning},
+ volume = {14},
+ copyright = {2017 Springer Nature America, Inc.},
+ issn = {1548-7105},
+ url = {https://www.nature.com/articles/nmeth.4207},
+ doi = {10.1038/nmeth.4207},
+ abstract = {The SIMLR software identifies similarities between cells across a range of single-cell RNA-seq data, enabling effective dimension reduction, clustering and visualization.},
+ language = {en},
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+ journal = {Nature Methods},
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+ month = apr,
+ year = {2017},
+ publisher = {Nature Publishing Group},
+ keywords = {Gene expression, Genome informatics, Machine learning, Statistical methods},
+ pages = {414--416},
+}
+
+
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-}
+ title = {Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity},
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+ year = {2019},
+ month = {Jun.},
+ journal = {Cell},
+ publisher = {Elsevier {BV}},
+ volume = {177},
+ number = {7},
+ pages = {1873--1887.e17},
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+}
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+}
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-}
+ title = {A single-cell and spatially resolved atlas of human breast cancers},
+ author = {Sunny Z. Wu and Ghamdan Al-Eryani and Daniel Lee Roden and Simon Junankar and Kate Harvey and Alma Andersson and Aatish Thennavan and Chenfei Wang and James R. Torpy and Nenad Bartonicek and Taopeng Wang and Ludvig Larsson and Dominik Kaczorowski and Neil I. Weisenfeld and Cedric R. Uytingco and Jennifer G. Chew and Zachary W. Bent and Chia-Ling Chan and Vikkitharan Gnanasambandapillai and Charles-Antoine Dutertre and Laurence Gluch and Mun N. Hui and Jane Beith and Andrew Parker and Elizabeth Robbins and Davendra Segara and Caroline Cooper and Cindy Mak and Belinda Chan and Sanjay Warrier and Florent Ginhoux and Ewan Millar and Joseph E. Powell and Stephen R. Williams and X. Shirley Liu and Sandra O'Toole and Elgene Lim and Joakim Lundeberg and Charles M. Perou and Alexander Swarbrick},
+ year = {2021},
+ month = {Sept.},
+ journal = {Nature Genetics},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {53},
+ number = {9},
+ pages = {1334--1347},
+ doi = {10.1038/s41588-021-00911-1},
+ url = {https://doi.org/10.1038/s41588-021-00911-1}
+}
+
+
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- volume = {11},
- doi = {10.3389/fgene.2020.00786},
- url = {https://doi.org/10.3389/fgene.2020.00786},
-}
+ title = {{NeuralEE}: A {GPU}-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale {scRNA}-Seq Data},
+ author = {Jiankang Xiong and Fuzhou Gong and Lin Wan and Liang Ma},
+ year = {2020},
+ month = {Oct.},
+ journal = {Frontiers in Genetics},
+ publisher = {Frontiers Media {SA}},
+ volume = {11},
+ doi = {10.3389/fgene.2020.00786},
+ url = {https://doi.org/10.3389/fgene.2020.00786}
+}
+
+
@article{xiong2021online,
- title = {Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space},
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- doi = {10.1038/s41467-022-33758-z},
- url = {https://doi.org/10.1038/s41467-022-33758-z},
-}
+ title = {Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space},
+ author = {Lei Xiong and Kang Tian and Yuzhe Li and Weixi Ning and Xin Gao and Qiangfeng Cliff Zhang},
+ year = {2022},
+ month = {Oct.},
+ journal = {Nature Communications},
+ publisher = {Springer Science and Business Media {LLC}},
+ volume = {13},
+ number = {1},
+ doi = {10.1038/s41467-022-33758-z},
+ url = {https://doi.org/10.1038/s41467-022-33758-z}
+}
+
+
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- volume = {17},
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- url = {https://doi.org/10.15252/msb.20209620},
-}
+ title = {Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models},
+ author = {Chenling Xu and Romain Lopez and Edouard Mehlman and Jeffrey Regier and Michael I Jordan and Nir Yosef},
+ year = {2021},
+ month = {Jan},
+ journal = {Molecular Systems Biology},
+ publisher = {{Embo}},
+ volume = {17},
+ number = {1},
+ doi = {10.15252/msb.20209620},
+ url = {https://doi.org/10.15252/msb.20209620}
+}
+
+
+@article{zappia2018exploring,
+ doi = {10.1371/journal.pcbi.1006245},
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+ year = {2018},
+ month = {Jun.},
+ publisher = {Public Library of Science ({PLoS})},
+ volume = {14},
+ number = {6},
+ pages = {e1006245},
+ author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
+ editor = {Dina Schneidman},
+ title = {Exploring the single-cell {RNA}-seq analysis landscape with the {scRNA}-tools database},
+ journal = {{PLOS} Computational Biology}
+}
+
+
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- url = {https://doi.org/10.1016/j.heliyon.2021.e06199},
+ title = {{pyDRMetrics} - A Python toolkit for dimensionality reduction quality assessment},
+ author = {Yinsheng Zhang and Qian Shang and Guoming Zhang},
+ year = {2021},
+ month = {Feb.},
+ journal = {Heliyon},
+ publisher = {Elsevier {BV}},
+ volume = {7},
+ number = {2},
+ pages = {e06199},
+ doi = {10.1016/j.heliyon.2021.e06199},
+ url = {https://doi.org/10.1016/j.heliyon.2021.e06199}
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+
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+ author = {Karin Hrovatin and Aim{\'e}e Bastidas-Ponce and Mostafa Bakhti and Luke Zappia and Maren B{\"u}ttner and Ciro Sallino and Michael Sterr and Anika B{\"o}ttcher and Adriana Migliorini and Heiko Lickert and Fabian J. Theis},
+ title = {Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas},
+ elocation-id = {2022.12.22.521557},
+ year = {2023},
+ doi = {10.1101/2022.12.22.521557},
+ publisher = {Cold Spring Harbor Laboratory},
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+ journal = {bioRxiv}
+}
+
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+ title = {An integrated cell atlas of the lung in health and disease},
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+ ISSN = {1546-170X},
+ url = {http://dx.doi.org/10.1038/s41591-023-02327-2},
+ DOI = {10.1038/s41591-023-02327-2},
+ number = {6},
+ journal = {Nature Medicine},
+ publisher = {Springer Science and Business Media LLC},
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+ year = {2023},
+ month = jun,
+ pages = {1563–1577}
+}
+
+@article{consortium2022tabula,
+ title = {The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans},
+ volume = {376},
+ ISSN = {1095-9203},
+ url = {http://dx.doi.org/10.1126/science.abl4896},
+ DOI = {10.1126/science.abl4896},
+ number = {6594},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science (AAAS)},
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+ year = {2022},
+ month = may
+}
+
+@article{dominguez2022crosstissue,
+ title = {Cross-tissue immune cell analysis reveals tissue-specific features in humans},
+ volume = {376},
+ ISSN = {1095-9203},
+ url = {http://dx.doi.org/10.1126/science.abl5197},
+ DOI = {10.1126/science.abl5197},
+ number = {6594},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science (AAAS)},
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+ year = {2022},
+ month = may
+}
+
+@article{eraslan2022singlenucleus,
+ title = {Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function},
+ volume = {376},
+ ISSN = {1095-9203},
+ url = {http://dx.doi.org/10.1126/science.abl4290},
+ DOI = {10.1126/science.abl4290},
+ number = {6594},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science (AAAS)},
+ author = {Eraslan, G\"{o}kcen and Drokhlyansky, Eugene and Anand, Shankara and Fiskin, Evgenij and Subramanian, Ayshwarya and Slyper, Michal and Wang, Jiali and Van Wittenberghe, Nicholas and Rouhana, John M. and Waldman, Julia and Ashenberg, Orr and Lek, Monkol and Dionne, Danielle and Win, Thet Su and Cuoco, Michael S. and Kuksenko, Olena and Tsankov, Alexander M. and Branton, Philip A. and Marshall, Jamie L. and Greka, Anna and Getz, Gad and Segrè, Ayellet V. and Aguet, Fran\c{c}ois and Rozenblatt-Rosen, Orit and Ardlie, Kristin G. and Regev, Aviv},
+ year = {2022},
+ month = may
+}
+
+@article{li2023integrated,
+ title = {Integrated multi-omics single cell atlas of the human retina},
+ url = {http://dx.doi.org/10.1101/2023.11.07.566105},
+ DOI = {10.1101/2023.11.07.566105},
+ publisher = {Cold Spring Harbor Laboratory},
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+ month = nov
+}
+
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+ title = {Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression},
+ volume = {13},
+ ISSN = {2041-1723},
+ url = {http://dx.doi.org/10.1038/s41467-022-32972-z},
+ DOI = {10.1038/s41467-022-32972-z},
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+ journal = {Nature Communications},
+ publisher = {Springer Science and Business Media LLC},
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+ year = {2022},
+ month = sep
+}
+
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+ title = {HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus},
+ volume = {4},
+ ISSN = {2522-5812},
+ url = {http://dx.doi.org/10.1038/s42255-022-00657-y},
+ DOI = {10.1038/s42255-022-00657-y},
+ number = {10},
+ journal = {Nature Metabolism},
+ publisher = {Springer Science and Business Media LLC},
+ author = {Steuernagel, Lukas and Lam, Brian Y. H. and Klemm, Paul and Dowsett, Georgina K. C. and Bauder, Corinna A. and Tadross, John A. and Hitschfeld, Tamara Sotelo and del Rio Martin, Almudena and Chen, Weiyi and de Solis, Alain J. and Fenselau, Henning and Davidsen, Peter and Cimino, Irene and Kohnke, Sara N. and Rimmington, Debra and Coll, Anthony P. and Beyer, Andreas and Yeo, Giles S. H. and Br\"{u}ning, Jens C.},
+ year = {2022},
+ month = oct,
+ pages = {1402–1419}
+}
+
+@article{tian2023singlecell,
+ title = {Single-cell DNA methylation and 3D genome architecture in the human brain},
+ volume = {382},
+ ISSN = {1095-9203},
+ url = {http://dx.doi.org/10.1126/science.adf5357},
+ DOI = {10.1126/science.adf5357},
+ number = {6667},
+ journal = {Science},
+ publisher = {American Association for the Advancement of Science (AAAS)},
+ author = {Tian, Wei and Zhou, Jingtian and Bartlett, Anna and Zeng, Qiurui and Liu, Hanqing and Castanon, Rosa G. and Kenworthy, Mia and Altshul, Jordan and Valadon, Cynthia and Aldridge, Andrew and Nery, Joseph R. and Chen, Huaming and Xu, Jiaying and Johnson, Nicholas D. and Lucero, Jacinta and Osteen, Julia K. and Emerson, Nora and Rink, Jon and Lee, Jasper and Li, Yang E. and Siletti, Kimberly and Liem, Michelle and Claffey, Naomi and O’Connor, Carolyn and Yanny, Anna Marie and Nyhus, Julie and Dee, Nick and Casper, Tamara and Shapovalova, Nadiya and Hirschstein, Daniel and Ding, Song-Lin and Hodge, Rebecca and Levi, Boaz P. and Keene, C. Dirk and Linnarsson, Sten and Lein, Ed and Ren, Bing and Behrens, M. Margarita and Ecker, Joseph R.},
+ year = {2023},
+ month = oct
}
diff --git a/results/_generate_task_pages.py b/results/_generate_task_pages.py
index eace4542..cb9db37d 100755
--- a/results/_generate_task_pages.py
+++ b/results/_generate_task_pages.py
@@ -19,8 +19,10 @@
title: "{task_name}"
subtitle: "{task_summary}"
engine: knitr
-image: featured.png
+image: thumbnail.svg
page-layout: full
+css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{{r}}
diff --git a/results/_include/_baseline_descriptions.qmd b/results/_include/_baseline_descriptions.qmd
index eaa0e50a..4c710a6c 100644
--- a/results/_include/_baseline_descriptions.qmd
+++ b/results/_include/_baseline_descriptions.qmd
@@ -1,8 +1,8 @@
-```{r}
+```{r baseline_descriptions}
#| echo: false
baselines <- method_info %>% filter(is_baseline)
lines <- pmap_chr(baselines, function(method_name, method_summary, reference, code_url, ...) {
- summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\. *$", "")
+ summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
glue::glue("* **{method_name}**: {summ}.")
})
knitr::asis_output(paste(lines, collapse = "\n"))
diff --git a/results/_include/_dataset_descriptions.qmd b/results/_include/_dataset_descriptions.qmd
index 0f5b70bd..26da13cd 100644
--- a/results/_include/_dataset_descriptions.qmd
+++ b/results/_include/_dataset_descriptions.qmd
@@ -1,13 +1,9 @@
-```{r}
+```{r dataset_description}
#| echo: false
lines <- pmap_chr(dataset_info, function(dataset_name, dataset_summary, data_reference, ...) {
- ref <-
- if (!is.na(data_reference)) {
- paste0("<sup>", cite_fun(data_reference, "html"), "</sup>")
- } else {
- ""
- }
- summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\. *$", "")
+ ref <- split_cite_fun(data_reference)
+ if (ref != "") ref <- paste0(" ", ref)
+ summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
glue::glue("* **{dataset_name}**{ref}: {summ}.")
})
knitr::asis_output(paste(lines, collapse = "\n"))
diff --git a/results/_include/_load_data.qmd b/results/_include/_load_data.qmd
index 15b2879c..50f88f20 100644
--- a/results/_include/_load_data.qmd
+++ b/results/_include/_load_data.qmd
@@ -10,7 +10,10 @@ library(kableExtra)
# read task info
task_info <- jsonlite::read_json(paste0(params$data_dir, "/task_info.json"))
+
+# add missing data
task_info$task_description <- task_info$task_description %||% NA_character_
+task_info$task_motivation <- task_info$task_motivation %||% NA_character_
`%|%` <- function(x, y) {
ifelse(is.na(x), y, x)
@@ -22,43 +25,37 @@ dataset_info <- jsonlite::read_json(paste0(params$data_dir, "/dataset_info.json"
results <- jsonlite::read_json(paste0(params$data_dir, "/results.json"), simplifyVector = TRUE)
qc <- jsonlite::read_json(paste0(params$data_dir, "/quality_control.json"), simplifyVector = TRUE)
+# add missing columns
for (col in c("method_summary")) {
method_info[[col]] <- method_info[[col]] %||% NA_character_
}
for (col in c("metric_summary")) {
metric_info[[col]] <- metric_info[[col]] %||% NA_character_
}
-for (col in c("dataset_summary")) {
+for (col in c("dataset_summary", "dataset_name")) {
dataset_info[[col]] <- dataset_info[[col]] %||% NA_character_
}
+# fill missing data
+dataset_info$dataset_name <- dataset_info$dataset_name %|% dataset_info$dataset_id
+
num_methods <- sum(!method_info$is_baseline)
num_baselines <- sum(method_info$is_baseline)
num_datasets <- nrow(dataset_info)
num_metrics <- nrow(metric_info)
+split_cite_fun <- function(keys) {
+ if (is.null(keys)) return("")
+
+ keys <- keys[!is.na(keys)]
+ if (length(keys) == 0) return("")
-link_fun <- function(label, url, format = "markdown") {
- if (format == "markdown") {
- paste0("[", label, "](", url, ")")
- } else {
- paste0("<a href=\"", url, "\" target=\"_blank\">", label, "</a>")
- }
+ refs <- unlist(stringr::str_split(keys, ", *"))
+ # inner_str <- sapply(refs, function(ref) cite_fun(ref, format = format))
+ # paste0("<sup>", paste(inner_str, collapse = ", "), "</sup>")
+ # paste0("[", paste(inner_str, collapse = ", "), "]")
+ paste0("[@", paste(refs, collapse = "; @"), "]")
}
-cite_map <- list()
-cite_fun <- function(key, format = "markdown") {
- # if (is.null(options("citation_map"))) {
- # options("citation_map" = list())
- # }
- # cm <- options("citation_map")
- if (!key %in% names(cite_map)) {
- cite_map[[key]] <<- length(cite_map) + 1
- # options("citation_map" = cm)
- }
- num <- cite_map[[key]]
- link_fun(num, paste0("/bibliography/#", key), format = format)
-}
-
```
diff --git a/results/_include/_method_descriptions.qmd b/results/_include/_method_descriptions.qmd
index 207124b5..7dfe475e 100644
--- a/results/_include/_method_descriptions.qmd
+++ b/results/_include/_method_descriptions.qmd
@@ -1,25 +1,27 @@
-```{r}
+```{r method_description}
#| echo: false
# show each method just once
lines <- pmap_chr(method_info, function(method_name, method_summary, paper_reference, code_url, code_version, ...) {
+
links <- c()
if (!is.na(code_url)) {
links <- c(links, glue::glue(" [Docs]({code_url})"))
}
version_label <-
- if (!is.na(code_version)) {
+ if (!is.na(code_version) && code_version != "missing-version") {
glue::glue(" Software version {code_version}.")
} else {
""
}
- ref <-
- if (!is.na(paper_reference)) {
- paste0("<sup>", cite_fun(paper_reference, "html"), "</sup>")
+ ref <- split_cite_fun(paper_reference)
+ if (ref != "") ref <- paste0(" ", ref)
+ links_label <-
+ if (length(links) > 0) {
+ glue::glue(" Links: {paste(links, collapse = ', ')}.")
} else {
""
}
- links_label <- glue::glue(" Links: {paste(links, collapse = ', ')}.")
- summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\. *$", "")
+ summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
glue::glue("* **{method_name}**{ref}: {summ}.{version_label}{links_label}")
})
knitr::asis_output(paste(lines, collapse = "\n"))
diff --git a/results/_include/_metric_descriptions.qmd b/results/_include/_metric_descriptions.qmd
index 98a5334a..3a0c9b2d 100644
--- a/results/_include/_metric_descriptions.qmd
+++ b/results/_include/_metric_descriptions.qmd
@@ -1,13 +1,9 @@
```{r}
#| echo: false
lines <- pmap_chr(metric_info, function(metric_name, metric_summary, paper_reference, ...) {
- ref <-
- if (!is.na(paper_reference)) {
- paste0("<sup>", cite_fun(paper_reference, "html"), "</sup>")
- } else {
- ""
- }
- summ <- (metric_summary %|% "Missing 'metric_summary'") %>% str_replace_all("\\. *$", "")
+ ref <- split_cite_fun(paper_reference)
+ if (ref != "") ref <- paste0(" ", ref)
+ summ <- (metric_summary %|% "Missing 'metric_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
glue::glue("* **{metric_name}**{ref}: {summ}.")
})
knitr::asis_output(paste(lines, collapse = "\n"))
diff --git a/results/_include/_results_table.qmd b/results/_include/_results_table.qmd
index c5fa6d22..0c3024ab 100644
--- a/results/_include/_results_table.qmd
+++ b/results/_include/_results_table.qmd
@@ -3,7 +3,7 @@ Results table of the scores per method, dataset and metric (after scaling). Use
```{r resultstable}
#| echo: false
res_tib0 <- results %>%
- unnest(scaled_scores) %>%
+ unnest(metric_values) %>%
unnest(resources) %>%
left_join(method_info %>% select(-commit_sha, -code_version, -task_id), by = "method_id") %>%
filter(!is_baseline) %>%
@@ -14,7 +14,7 @@ mean_na_zero <- function(x) {
}
res_tib1 <- res_tib0 %>%
- group_by(method_id, method_name, paper_reference, code_url, code_version) %>%
+ group_by(method_id, method_name, paper_reference, code_url) %>%
summarise_if(is.numeric, mean_na_zero) %>%
ungroup() %>%
mutate(
@@ -27,16 +27,12 @@ res_tib <- res_tib1 %>%
arrange(desc(mean_score)) %>%
rowwise() %>%
mutate(
- method_label = ifelse(is.na(paper_reference), method_name, glue::glue("{method_name} <sup>{cite_fun(paper_reference, format = 'html')}</sup>")),
- dataset_label = ifelse(is.na(data_reference), dataset_name, glue::glue("{dataset_name} <sup>{cite_fun(data_reference, format = 'html')}</sup>")),
- # method_label = method_name,
- # dataset_label = dataset_name,
peak_memory_gb = peak_memory_mb / 1024
) %>%
ungroup() %>%
select(
- method_label,
- dataset_label,
+ method_name,
+ dataset_name,
mean_score,
any_of(metric_info$metric_id),
duration_sec,
diff --git a/results/_include/_summary_figure.qmd b/results/_include/_summary_figure.qmd
index 34cf4a14..845117fb 100644
--- a/results/_include/_summary_figure.qmd
+++ b/results/_include/_summary_figure.qmd
@@ -95,10 +95,12 @@ palettes <- list(
# column_info = column_info %>% filter(id %in% colnames(summary_all)),
# column_groups = column_groups,
# palettes = palettes,
-# # determine xmax expand heuristically
-# expand = c(xmax = max(str_length(tail(column_info$name, 4))) / 5),
-# # determine offset heuristically
-# col_annot_offset = max(str_length(column_info$name)) / 5,
+# position_args = position_arguments(
+# # determine xmax expand heuristically
+# expand_xmax = max(str_length(tail(column_info$name, 4))) / 5,
+# # determine offset heuristically
+# col_annot_offset = max(str_length(column_info$name)) / 5
+# ),
# add_abc = FALSE,
# scale_column = FALSE
# )
diff --git a/results/_include/_task_template.qmd b/results/_include/_task_template.qmd
index 7dd417e8..f8cad901 100644
--- a/results/_include/_task_template.qmd
+++ b/results/_include/_task_template.qmd
@@ -5,8 +5,17 @@
`r num_methods` methods • `r num_metrics` metrics • `r num_datasets` datasets
:::
-## Description
-`r task_info$task_description %|% "Missing 'task_description'"`
+Data:
+<a href="data/task_info.json" class="btn btn-secondary">Task info</a>
+<a href="data/method_info.json" class="btn btn-secondary">Method info</a>
+<a href="data/metric_info.json" class="btn btn-secondary">Metric info</a>
+<a href="data/dataset_info.json" class="btn btn-secondary">Dataset info</a>
+<a href="data/results.json" class="btn btn-secondary">Results</a>
+<a href="data/quality_control.json" class="btn btn-secondary">Quality control</a>
+
+`r task_info$task_motivation %|% ""`
+
+`r task_info$task_description %|% ""`
## Summary
@@ -40,19 +49,6 @@
</details>
-
-<details><summary>Download raw data</summary>
-
-<a href="data/task_info.json" class="btn btn-secondary">Task info</a>
-<a href="data/method_info.json" class="btn btn-secondary">Method info</a>
-<a href="data/metric_info.json" class="btn btn-secondary">Metric info</a>
-<a href="data/dataset_info.json" class="btn btn-secondary">Dataset info</a>
-<a href="data/results.json" class="btn btn-secondary">Results</a>
-<a href="data/quality_control.json" class="btn btn-secondary">Quality control</a>
-
-</details>
-
-
<details><summary>Quality control results</summary>
{{< include ../_include/_qc_table.qmd >}}
diff --git a/results/batch_integration_embed/index.qmd b/results/batch_integration_embed/index.qmd
index bea99567..351e3571 100644
--- a/results/batch_integration_embed/index.qmd
+++ b/results/batch_integration_embed/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/batch_integration_feature/index.qmd b/results/batch_integration_feature/index.qmd
index 4887b63a..4ce15598 100644
--- a/results/batch_integration_feature/index.qmd
+++ b/results/batch_integration_feature/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/batch_integration_graph/index.qmd b/results/batch_integration_graph/index.qmd
index c49968d9..7fa6a9e7 100644
--- a/results/batch_integration_graph/index.qmd
+++ b/results/batch_integration_graph/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/cell_cell_communication_ligand_target/index.qmd b/results/cell_cell_communication_ligand_target/index.qmd
index 2f5f56d0..d0f6c93c 100644
--- a/results/cell_cell_communication_ligand_target/index.qmd
+++ b/results/cell_cell_communication_ligand_target/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/cell_cell_communication_source_target/index.qmd b/results/cell_cell_communication_source_target/index.qmd
index 9c2c897f..c21d4db1 100644
--- a/results/cell_cell_communication_source_target/index.qmd
+++ b/results/cell_cell_communication_source_target/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/denoising/index.qmd b/results/denoising/index.qmd
index 3258fdda..e78f25f2 100644
--- a/results/denoising/index.qmd
+++ b/results/denoising/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/dimensionality_reduction/index.qmd b/results/dimensionality_reduction/index.qmd
index ac7264f1..0f37be63 100644
--- a/results/dimensionality_reduction/index.qmd
+++ b/results/dimensionality_reduction/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/label_projection/index.qmd b/results/label_projection/index.qmd
index 2abca097..d30f4b31 100644
--- a/results/label_projection/index.qmd
+++ b/results/label_projection/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/matching_modalities/index.qmd b/results/matching_modalities/index.qmd
index 08e4e8d6..b38801d1 100644
--- a/results/matching_modalities/index.qmd
+++ b/results/matching_modalities/index.qmd
@@ -1,10 +1,11 @@
---
-title: "Matching modalities"
+title: "Multimodal Data Integration"
subtitle: "Alignment of cellular profiles from two different modalities"
engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}
diff --git a/results/multimodal_data_integration/data/results.json b/results/multimodal_data_integration/data/results.json
deleted file mode 100644
index 20ec2b2d..00000000
--- a/results/multimodal_data_integration/data/results.json
+++ /dev/null
@@ -1,506 +0,0 @@
-[
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "true_features",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:05.094",
- "code_version": "0.6.0",
- "resources": {
- "duration_sec": 280.0,
- "cpu_pct": 144.8,
- "peak_memory_mb": 581.2,
- "disk_read_mb": 232.9,
- "disk_write_mb": 277.4
- },
- "metric_values": {
- "knn_auc": 0.5446604149777994,
- "mse": 0.0
- },
- "scaled_scores": {
- "knn_auc": 1.0,
- "mse": 1.0
- },
- "mean_score": 1.0
- },
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "procrustes",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:05.062",
- "code_version": "1.9.3",
- "resources": {
- "duration_sec": 291.0,
- "cpu_pct": 132.8,
- "peak_memory_mb": 580.2,
- "disk_read_mb": 232.9,
- "disk_write_mb": 278.6
- },
- "metric_values": {
- "knn_auc": 0.202456607136907,
- "mse": 0.5721031343678257
- },
- "scaled_scores": {
- "knn_auc": 0.3081717049068007,
- "mse": 0.4265716152922763
- },
- "mean_score": 0.3673716600995385
- },
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "random_features",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:05.165",
- "code_version": "0.6.0",
- "resources": {
- "duration_sec": 321.0,
- "cpu_pct": 81.0,
- "peak_memory_mb": 580.2,
- "disk_read_mb": 232.9,
- "disk_write_mb": 277.4
- },
- "metric_values": {
- "knn_auc": 0.05002350829448345,
- "mse": 0.9976889
- },
- "scaled_scores": {
- "knn_auc": 0.0,
- "mse": 0.0
- },
- "mean_score": 0.0
- },
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "mnn_log_cpm",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:04.984",
- "code_version": "1.12.3",
- "resources": {
- "duration_sec": 540.0,
- "cpu_pct": 43.5,
- "peak_memory_mb": 2000.0,
- "disk_read_mb": 276.6,
- "disk_write_mb": 369.5
- },
- "metric_values": {
- "knn_auc": 0.056963681971617865,
- "mse": 0.8873942719615318
- },
- "scaled_scores": {
- "knn_auc": 0.014030844814371599,
- "mse": 0.11055012042177503
- },
- "mean_score": 0.062290482618073316
- },
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "mnn_log_scran_pooling",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:04.921",
- "code_version": "1.12.3",
- "resources": {
- "duration_sec": 830.0,
- "cpu_pct": 77.7,
- "peak_memory_mb": 4300.0,
- "disk_read_mb": 279.4,
- "disk_write_mb": 369.6
- },
- "metric_values": {
- "knn_auc": 0.043650253881415725,
- "mse": 1.013315474905537
- },
- "scaled_scores": {
- "knn_auc": -0.012884712658831402,
- "mse": -0.015662773140542097
- },
- "mean_score": -0.01427374289968675
- },
- {
- "task_id": "multimodal_data_integration",
- "commit_sha": "a49ae996dc5f34402b1fa5cab9b3a3936126a413",
- "method_id": "harmonic_alignment_sqrt_cpm",
- "dataset_id": "citeseq_cbmc",
- "submission_time": "2022-12-14 10:26:04.848",
- "code_version": "0.0",
- "resources": {
- "duration_sec": 890.0,
- "cpu_pct": 903.9,
- "peak_memory_mb": 627.9,
- "disk_read_mb": 232.2,
- "disk_write_mb": 290.1
- },
- "metric_values": {
- "knn_auc": 0.04945913147626341,
- "mse": 1.0000115280311805
- },
- "scaled_scores": {
- "knn_auc": -0.0011409921309842325,
- "mse": -0.002328008291142103
- },
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\ No newline at end of file
diff --git a/results/spatial_decomposition/index.qmd b/results/spatial_decomposition/index.qmd
index eda7c348..077e80af 100644
--- a/results/spatial_decomposition/index.qmd
+++ b/results/spatial_decomposition/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
image: thumbnail.svg
page-layout: full
css: ../task_template.css
+bibliography: ../../bibliography/library.bib
---
```{r}