References#
Malte Luecken, Daniel Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann Chen, Louise Deconinck, Angela Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Kim, Dominik Klein, BONY DE KUMAR, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Joaquin Melgarejo, Honey Mekonen, Maurizio Morri, Michaela Müller, Norma Neff, Sheryl Paul, Bastian Rieck, Kaylie Schneider, Scott Steelman, Michael Sterr, Daniel Treacy, Alexander Tong, Alexandra-Chloe Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela Pisco, Smita Krishnaswamy, Fabian Theis, and Jonathan M Bloom. A sandbox for prediction and integration of dna, rna, and proteins in single cells. In J. Vanschoren and S. Yeung, editors, Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks, volume 1. Curran, 2021. URL: https://datasets-benchmarks-proceedings.neurips.cc/paper_files/paper/2021/file/158f3069a435b314a80bdcb024f8e422-Paper-round2.pdf.
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, and Quin F Wills. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in r. Bioinformatics, 33(8):1179–1186, January 2017. URL: https://doi.org/10.1093/bioinformatics/btw777, doi:10.1093/bioinformatics/btw777.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, and Aviv Regev. Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33(5):495–502, April 2015. URL: https://doi.org/10.1038/nbt.3192, doi:10.1038/nbt.3192.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, and Rahul Satija. Comprehensive integration of single-cell data. Cell, 177(7):1888–1902, 2019.
Vincent A Traag, Ludo Waltman, and Nees Jan Van Eck. From louvain to leiden: guaranteeing well-connected communities. Scientific reports, 9(1):5233, 2019.
Samuel L. Wolock, Romain Lopez, and Allon M. Klein. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Systems, 8(4):281–291.e9, April 2019. URL: https://doi.org/10.1016/j.cels.2018.11.005, doi:10.1016/j.cels.2018.11.005.
Grace X. Y. Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark T. Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Donald A. Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W. Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan W. Beppu, H. Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson, and Jason H. Bielas. Massively parallel digital transcriptional profiling of single cells. Nature Communications, January 2017. URL: https://doi.org/10.1038/ncomms14049, doi:10.1038/ncomms14049.