The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
Tutorials provided for three types of analysis performed by the package:
- Clustering, classifying, and counting cells
- Constructing single-cell trajectories
- Differential expression analysis
Cole Trapnell*, Davide Cacchiarelli*, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J. Lennon, Kenneth J. Livak, Tarjei S. Mikkelsen, and John L. Rinn. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology, 2014.
Junyue Cao*, Jonathan S. Packer*, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N. Furlan, Frank J. Steemers, Andrew Adey, Robert H. Waterston, Cole Trapnell**, Jay Shendure** . Comprehensive single-cell transcriptional profiling of a multicellular organism. Science, 2017.
Jacob H. Levine, Erin F. Simonds, Sean C. Bendall, Kara L. Davis, El-ad D. Amir, Michelle Tadmor, Oren Litvin, Harris Fienberg, Astraea Jager, Eli Zunder, Rachel Finck, Amanda L. Gedman, Ina Radtke, James R. Downing, Dana Pe’er** and Garry P. Nolan**. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell, 2015.
F. Alexander Wolf,, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon and Fabian J. Theis PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome biology, 2018.
Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing well-connected communities. Scientific Reports, 2019.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan & John C Marioni Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nature Biotechnology, 2018.
Junyue Cao*, Malte Spielmann*, Xiaojie Qiu, Xingfan Huang, Daniel M. Ibrahim, Andrew J. Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J. Steemers, Cole Trapnell**, and Jay Shendure** The single-cell transcriptional landscape of mammalian organogenesis. Nature, 2019.
Jonathan S. Packer*, Qin Zhu*, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim**, Robert H. Waterston**, John I. Murray** A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution. Science, 2019.
Nadav Sharon*, Raghav Chawla*, Jonas Mueller, Jordan Vanderhooft, Luke James Whitehorn, Benjamin Rosenthal, Mads Gurtler, Ralph R. Estanboulieh, Dmitry Shvartsman, David K. Gifford, Cole Trapnell** and Doug Melton** A peninsular structure coordinates asynchronous differentiation with morphogenesis to generate pancreatic islets. Cell, 2019.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah Pliner, and Cole Trapnell Reversed graph embedding resolves complex single-cell developmental trajectories. Nature methods, 2017
X Qiu, A Hill, J Packer, D Lin, YA Ma, and C Trapnell. Single-cell mrna quantification and differential analysis with census. Nature methods, 2017
Haghverdi L, Lun ATL, Morgan MD, Marioni JC (2018). 'Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.' Nat. Biotechnol., 36(5), 421-427. doi: 10.1038/nbt.4091