forked from scverse/scanpy
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
0370057
commit dbea062
Showing
7 changed files
with
62 additions
and
60 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,100 +1,104 @@ | ||
| @inproceedings{luecken2021, | ||
| 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}, | ||
| @inproceedings{Luecken2021, | ||
| 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}, | ||
| editor = {Vanschoren, J. and Yeung, S.}, | ||
| 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} | ||
| year = {2021}, | ||
| } | ||
|
|
||
| @article{McCarthy2017, | ||
| author = {McCarthy, Davis J and Campbell, Kieran R and Lun, Aaron T L and Wills, Quin F}, | ||
| editor = {Hofacker, Ivo}, | ||
| doi = {10.1093/bioinformatics/btw777}, | ||
| url = {https://doi.org/10.1093/bioinformatics/btw777}, | ||
| year = {2017}, | ||
| month = jan, | ||
| month = {jan}, | ||
| publisher = {Oxford University Press ({OUP})}, | ||
| volume = {33}, | ||
| number = {8}, | ||
| pages = {1179--1186}, | ||
| author = {Davis J McCarthy and Kieran R Campbell and Aaron T L Lun and Quin F Wills}, | ||
| editor = {Ivo Hofacker}, | ||
| title = {Scater: pre-processing, quality control, normalization and visualization of single-cell {RNA}-seq data in R}, | ||
| journal = {Bioinformatics} | ||
| title = {Scater: pre-processing, quality control, normalization and visualization of single-cell {RNA}-seq data in R}, | ||
| journal = {Bioinformatics}, | ||
| } | ||
|
|
||
| @article{Satija2015, | ||
| author = {Satija, Rahul and Farrell, Jeffrey A and Gennert, David and Schier, Alexander F and Regev, Aviv}, | ||
| doi = {10.1038/nbt.3192}, | ||
| url = {https://doi.org/10.1038/nbt.3192}, | ||
| year = {2015}, | ||
| month = apr, | ||
| month = {apr}, | ||
| publisher = {Springer Science and Business Media {LLC}}, | ||
| volume = {33}, | ||
| number = {5}, | ||
| pages = {495--502}, | ||
| author = {Rahul Satija and Jeffrey A Farrell and David Gennert and Alexander F Schier and Aviv Regev}, | ||
| title = {Spatial reconstruction of single-cell gene expression data}, | ||
| journal = {Nature Biotechnology} | ||
| journal = {Nature Biotechnology}, | ||
| } | ||
| @article{stuart2019comprehensive, | ||
| title = {Comprehensive integration of single-cell data}, | ||
|
|
||
| @article{Stuart2019, | ||
| author = {Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck, William M and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul}, | ||
| title = {Comprehensive integration of single-cell data}, | ||
| journal = {Cell}, | ||
| volume = {177}, | ||
| number = {7}, | ||
| pages = {1888--1902}, | ||
| year = {2019}, | ||
| publisher = {Elsevier} | ||
| publisher = {Elsevier}, | ||
| } | ||
| @article{traag2019louvain, | ||
| title = {From Louvain to Leiden: guaranteeing well-connected communities}, | ||
|
|
||
| @article{Traag2019, | ||
| author = {Traag, Vincent A and Waltman, Ludo and Van Eck, Nees Jan}, | ||
| title = {From Louvain to Leiden: guaranteeing well-connected communities}, | ||
| journal = {Scientific reports}, | ||
| volume = {9}, | ||
| number = {1}, | ||
| pages = {5233}, | ||
| year = {2019}, | ||
| publisher = {Nature Publishing Group UK London} | ||
| publisher = {Nature Publishing Group UK London}, | ||
| } | ||
|
|
||
| @article{Wolf2018, | ||
| author = {Wolf, F. Alexander | ||
| and Angerer, Philipp | ||
| and Theis, Fabian J.}, | ||
| title = {SCANPY: large-scale single-cell gene expression data analysis}, | ||
| journal = {Genome Biology}, | ||
| year = {2018}, | ||
| month = {Feb}, | ||
| day = {06}, | ||
| volume = {19}, | ||
| number = {1}, | ||
| pages = {15}, | ||
| abstract = {Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (https://github.com/theislab/Scanpy). Along with Scanpy, we present AnnData, a generic class for handling annotated data matrices (https://github.com/theislab/anndata).}, | ||
| issn = {1474-760X}, | ||
| doi = {10.1186/s13059-017-1382-0}, | ||
| url = {https://doi.org/10.1186/s13059-017-1382-0} | ||
| author = {Wolf, F. Alexander and Angerer, Philipp and Theis, Fabian J.}, | ||
| title = {SCANPY: large-scale single-cell gene expression data analysis}, | ||
| journal = {Genome Biology}, | ||
| year = {2018}, | ||
| month = {feb}, | ||
| day = {06}, | ||
| volume = {19}, | ||
| number = {1}, | ||
| pages = {15}, | ||
| issn = {1474-760X}, | ||
| doi = {10.1186/s13059-017-1382-0}, | ||
| url = {https://doi.org/10.1186/s13059-017-1382-0}, | ||
| } | ||
|
|
||
| @article{Wolock2019, | ||
| author = {Wolock, Samuel L. and Lopez, Romain and Klein, Allon M.}, | ||
| doi = {10.1016/j.cels.2018.11.005}, | ||
| url = {https://doi.org/10.1016/j.cels.2018.11.005}, | ||
| year = {2019}, | ||
| month = apr, | ||
| month = {apr}, | ||
| publisher = {Elsevier {BV}}, | ||
| volume = {8}, | ||
| number = {4}, | ||
| pages = {281--291.e9}, | ||
| author = {Samuel L. Wolock and Romain Lopez and Allon M. Klein}, | ||
| title = {Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data}, | ||
| journal = {Cell Systems} | ||
| journal = {Cell Systems}, | ||
| } | ||
|
|
||
| @article{Zheng2017, | ||
| author = {Zheng, Grace X. Y. and Terry, Jessica M. and Belgrader, Phillip and Ryvkin, Paul and Bent, Zachary W. and Wilson, Ryan and Ziraldo, Solongo B. and Wheeler, Tobias D. and McDermott, Geoff P. and Zhu, Junjie and Gregory, Mark T. and Shuga, Joe and Montesclaros, Luz and Underwood, Jason G. and Masquelier, Donald A. and Nishimura, Stefanie Y. and Schnall-Levin, Michael and Wyatt, Paul W. and Hindson, Christopher M. and Bharadwaj, Rajiv and Wong, Alexander and Ness, Kevin D. and Beppu, Lan W. and Deeg, H. Joachim and McFarland, Christopher and Loeb, Keith R. and Valente, William J. and Ericson, Nolan G. and Stevens, Emily A. and Radich, Jerald P. and Mikkelsen, Tarjei S. and Hindson, Benjamin J. and Bielas, Jason H.}, | ||
| doi = {10.1038/ncomms14049}, | ||
| url = {https://doi.org/10.1038/ncomms14049}, | ||
| year = {2017}, | ||
| month = jan, | ||
| month = {jan}, | ||
| publisher = {Springer Science and Business Media {LLC}}, | ||
| volume = {8}, | ||
| number = {1}, | ||
| author = {Grace X. Y. Zheng and Jessica M. Terry and Phillip Belgrader and Paul Ryvkin and Zachary W. Bent and Ryan Wilson and Solongo B. Ziraldo and Tobias D. Wheeler and Geoff P. McDermott and Junjie Zhu and Mark T. Gregory and Joe Shuga and Luz Montesclaros and Jason G. Underwood and Donald A. Masquelier and Stefanie Y. Nishimura and Michael Schnall-Levin and Paul W. Wyatt and Christopher M. Hindson and Rajiv Bharadwaj and Alexander Wong and Kevin D. Ness and Lan W. Beppu and H. Joachim Deeg and Christopher McFarland and Keith R. Loeb and William J. Valente and Nolan G. Ericson and Emily A. Stevens and Jerald P. Radich and Tarjei S. Mikkelsen and Benjamin J. Hindson and Jason H. Bielas}, | ||
| title = {Massively parallel digital transcriptional profiling of single cells}, | ||
| journal = {Nature Communications} | ||
| journal = {Nature Communications}, | ||
| } |