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book.bib
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book.bib
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@Book{xie2015,
title = {Dynamic Documents with {R} and knitr},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2015},
edition = {2nd},
note = {ISBN 978-1498716963},
url = {http://yihui.name/knitr/},
}
## 10-Cluster-Analysis #################
@article{soneson2018bias,
title={Bias, robustness and scalability in single-cell differential expression analysis},
author={Soneson, Charlotte and Robinson, Mark D},
journal={Nature methods},
volume={15},
number={4},
pages={255},
year={2018},
publisher={Nature Publishing Group}
}
@article{hedlund2018single,
title={Single-cell RNA sequencing: technical advancements and biological applications},
author={Hedlund, Eva and Deng, Qiaolin},
journal={Molecular aspects of medicine},
volume={59},
pages={36--46},
year={2018},
publisher={Elsevier}
}
## 14-Pseudotime #######################
@article{haghverdi2015diffusion,
title={Diffusion maps for high-dimensional single-cell analysis of differentiation data},
author={Haghverdi, Laleh and Buettner, Florian and Theis, Fabian J},
journal={Bioinformatics},
volume={31},
number={18},
pages={2989--2998},
year={2015},
publisher={Oxford University Press}
}
@article{haghverdi2016diffusion,
title={Diffusion pseudotime robustly reconstructs lineage branching},
author={Haghverdi, Laleh and Buettner, Maren and Wolf, F Alexander and Buettner, Florian and Theis, Fabian J},
journal={Nature methods},
volume={13},
number={10},
pages={845},
year={2016},
publisher={Nature Publishing Group}
}
@article{saelens2018comparison,
title={A comparison of single-cell trajectory inference methods: towards more accurate and robust tools},
author={Saelens, Wouter and Cannoodt, Robrecht and Todorov, Helena and Saeys, Yvan},
journal={bioRxiv},
pages={276907},
year={2018},
publisher={Cold Spring Harbor Laboratory}
}
@article{street2018slingshot,
title={Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics},
author={Street, Kelly and Risso, Davide and Fletcher, Russell B and Das, Diya and Ngai, John and Yosef, Nir and Purdom, Elizabeth and Dudoit, Sandrine},
journal={BMC genomics},
volume={19},
number={1},
pages={477},
year={2018},
publisher={BioMed Central}
}
@article{ji2016tscan,
title={TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis},
author={Ji, Zhicheng and Ji, Hongkai},
journal={Nucleic acids research},
volume={44},
number={13},
pages={e117--e117},
year={2016},
publisher={Oxford University Press}
}
@article{trapnell2014dynamics,
title={The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells},
author={Trapnell, Cole and Cacchiarelli, Davide and Grimsby, Jonna and Pokharel, Prapti and Li, Shuqiang and Morse, Michael and Lennon, Niall J and Livak, Kenneth J and Mikkelsen, Tarjei S and Rinn, John L},
journal={Nature biotechnology},
volume={32},
number={4},
pages={381},
year={2014},
publisher={Nature Publishing Group}
}
@article{schiebinger2019optimal,
title={Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming},
author={Schiebinger, Geoffrey and Shu, Jian and Tabaka, Marcin and Cleary, Brian and Subramanian, Vidya and Solomon, Aryeh and Gould, Joshua and Liu, Siyan and Lin, Stacie and Berube, Peter and others},
journal={Cell},
year={2019},
publisher={Elsevier}
}
@article{la2018rna,
title={RNA velocity of single cells},
author={La Manno, Gioele and Soldatov, Ruslan and Zeisel, Amit and Braun, Emelie and Hochgerner, Hannah and Petukhov, Viktor and Lidschreiber, Katja and Kastriti, Maria E and L{\"o}nnerberg, Peter and Furlan, Alessandro and others},
journal={Nature},
volume={560},
number={7719},
pages={494},
year={2018},
publisher={Nature Publishing Group}
}