Citations and Acknowledgements

Cite your analysis using get_citations

Monocle 3 utilizes methods published by other groups. Please be sure to cite those original methods papers when you use them in your analyses. To make this easier, we provide a function get_citations that will print a data frame with the methods and citations that you used in constructing your CDS object. As you use new methods, they will be added to your citation metadata.


# Your analysis used methods from the following recent work. Please cite them wherever you are presenting your analyses.
#    method       citations
# 1 Monocle       Trapnell C. et. al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).
# 2 Monocle       Qiu, X. et. al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).
# 3 Monocle       Cao, J. et. al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
# 4    UMAP       McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at (2018).


Monocle was originally built by Cole Trapnell and Davide Cacchiarelli, with substantial design input from John Rinn and Tarjei Mikkelsen. We are grateful to Sharif Bordbar, Chris Zhu, Amy Wagers and the Broad RNAi platform for technical assistance, and Magali Soumillon for helpful discussions. Cole Trapnell was supported by a Damon Runyon Postdoctoral Fellowship. Davide Cacchiarelli was supported by a Human Frontier Science Program Fellowship. Cacchiarelli and Mikkelsen were also supported by the Harvard Stem Cell Institute. John Rinn was the Alvin and Esta Star Associate Professor. This work was supported by NIH grants 1DP2OD00667, P01GM099117, and P50HG006193-01. This work was also supported in part by the Single Cell Genomics initiative, a collaboration between the Broad Institute and Fluidigm Inc.

Monocle versions 2 and 3 were developed by Cole Trapnell's lab. Significant portions were written by Xiaojie Qiu and Hannah Pliner. The work was supported by NIH grant 1DP2HD088158, the W. M. Keck Foundation, as well as an Alfred P. Sloan Foundation Research Fellowship. Hannah Pliner is supported by the Brotman Baty Institute.


  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Traag, V.A., Waltman, L. & van Eck, N.J.
    From Louvain to Leiden: guaranteeing well-connected communities.
    Scientific Reports, 2019.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

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