scmap: projection of single-cell RNA-seq data across data sets

Vladimir Yu Kiselev; Andrew Yiu; Martin Hemberg

doi:10.1038/nmeth.4644

Abstract

Single-cell RNA-seq (scRNA-seq) allows researchers to define cell types on the basis of unsupervised clustering of the transcriptome. However, differences in experimental methods and computational analyses make it challenging to compare data across experiments. Here we present scmap (http://bioconductor.org/packages/scmap; web version at http://www.sanger.ac.uk/science/tools/scmap), a method for projecting cells from an scRNA-seq data set onto cell types or individual cells from other experiments.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

Rent or Buy

All prices are NET prices.

References

1.
Regev, A. et al. eLife 6, e27041 (2017).
2.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. J. Mol. Biol. 215, 403–410 (1990).
3.
Jégou, H., Douze, M. & Schmid, C. IEEE Trans. Pattern Anal. Mach. Intell. 33, 117–128 (2011).
4.
Andrews, T.S. & Hemberg, M. BioRxiv. Preprint at https://www.biorxiv.org/content/early/2017/05/25/065094 (2016).
- - Google Scholar
5.
Brennecke, P. et al. Nat. Methods 10, 1093–1095 (2013).
6.
Cohen, J. Psychol. Bull. 70, 213–220 (1968).
7.
Picelli, S. et al. Nat. Protoc. 9, 171–181 (2014).
8.
Hashimshony, T. et al. Genome Biol. 17, 77 (2016).
9.
Klein, A.M. et al. Cell 161, 1187–1201 (2015).
10.
Wagner, A., Regev, A. & Yosef, N. Nat. Biotechnol. 34, 1145–1160 (2016).
11.
Trapnell, C. et al. Nat. Biotechnol. 32, 381–386 (2014).
12.
Jang, S. et al. elife 6, e20487 (2017).
13.
Treutlein, B. et al. Nature 534, 391–395 (2016).
14.
La Manno, G. et al. Cell 167, 566–580 (2016).
15.
Tung, P.-Y. Sci. Rep. 7, 39921 (2017).
16.
Camp, J.G. et al. Nature 546, 533–538 (2017).
- - PubMed
  - Google Scholar
17.
Crow, M., Paul, A., Ballouz, S., Huang, Z.J. & Gillis, J. Nat. Commun. 9, 884 (2018).
18.
Baron, M. et al. Cell Syst. 3, 346–360 (2016).
19.
Xin, Y. et al. Cell Metab. 24, 608–615 (2016).
20.
Segerstolpe, Å. et al. Cell Metab. 24, 593–607 (2016).
21.
McCarthy, D.J., Campbell, K.R., Lun, A.T.L. & Wills, Q.F. Bioinformatics 33, 1179–1186 (2017).
- - PubMed
  - Google Scholar
22.
Butler, A. & Satija, R. BioRxiv. Preprint at https://www.biorxiv.org/content/early/2017/07/18/164889 (2017).
- - Google Scholar
23.
Haghverdi, L., Lun, A.T.L., Morgan, M.D. & Marioni, J.C. bioRxiv Preprint at https://www.biorxiv.org/content/early/2017/07/18/165118 (2017).
- - Google Scholar
24.
Shekhar, K. et al. Cell 166, 1308–1323 (2016).
25.
Macosko, E.Z. et al. Cell 161, 1202–1214 (2015).
26.
Muraro, M.J. et al. Cell Syst. 3, 385–394 (2016).
27.
Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Science 343, 193–196 (2014).
28.
Yan, L. et al. Nat. Struct. Mol. Biol. 20, 1131–1139 (2013).
29.
Ben-Hur, A., Horn, D., Siegelmann, H.T. & Vapnik, V. J. Mach. Learn. Res. 2, 125–137 (2001).
- - Google Scholar
30.
Breiman, L. Mach. Learn. 45, 5–32 (2001).
- - Article
  - Google Scholar

Download references

Acknowledgements

We thank T. Andrews, K.N. Natarajan, G. Parada, M. Schaub, M. Stubbington, V. Svensson, J. Westoby and F. Wünnermann for helpful discussions, feedback on the manuscript and testing of the cloud implementation of scmap. Amazon Web Services (AWS) Cloud provided credits for running the scmap server for 1 year. V.Y.K., A.Y. and M.H. were supported by core funding to the Wellcome Sanger Institute provided by the Wellcome Trust.

Author information

Affiliations

Wellcome Sanger Institute, Hinxton, UK.
- Vladimir Yu Kiselev
- , Andrew Yiu
- & Martin Hemberg

Authors

Search for Vladimir Yu Kiselev in:
- Nature Research journals •
- PubMed •
- Google Scholar
Search for Andrew Yiu in:
- Nature Research journals •
- PubMed •
- Google Scholar
Search for Martin Hemberg in:
- Nature Research journals •
- PubMed •
- Google Scholar

Contributions

M.H. conceived the study and supervised the research; V.Y.K., A.Y. and M.H. contributed to the computational framework; V.Y.K. and M.H. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Martin Hemberg.

Integrated supplementary information

Supplementary figures

Supplementary information

PDF files

1.
Supplementary Text and Figures
Supplementary Figures 1–4, Supplementary Tables 1–3 and Supplementary Notes 1–2
2.
Life Sciences Reporting Summary

Zip files

1.
Supplementary Software
scmap software

Rights and permissions

To obtain permission to re-use content from this article visit RightsLink.

About this article

Publication history

Received

26 July 2017

Accepted

09 March 2018

Published

02 April 2018

DOI

https://doi.org/10.1038/nmeth.4644

Subjects