Scmap: Projection of single-cell RNA-seq data across data sets

Nature Methods

Volumn 15, Issue 5, 2018, Pages 359-362

  Kiselev, Vladimir Yu ^a   Yiu, Andrew ^a   Hemberg, Martin ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA; TRANSCRIPTOME;

AMINO ACID SEQUENCE; ARTICLE; CELL DIFFERENTIATION; CELL PROTECTION; CELL SELECTION; CELLS BY BODY ANATOMY; CLASSIFIER; EXPRESSION VECTOR; GENE; GENE EXPRESSION; HIGHLY VARIABLE GENE; K NEAREST NEIGHBOR; NONHUMAN; PRIORITY JOURNAL; RANDOM FOREST; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SINGLE CELL ANALYSIS; SOFTWARE; STATISTICAL MODEL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; PHYSIOLOGY; PROCEDURES;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; SINGLE-CELL ANALYSIS; SOFTWARE; TRANSCRIPTOME;

EID: 85046289245     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.4644     Document Type: Article

References (30)

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).
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).
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).
22. Butler, A. & Satija, R. BioRxiv. Preprint at https://www.biorxiv.org/content/early/2017/07/18/164889 (2017).
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).
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).
30. Breiman, L. Mach. Learn. 45, 5-32 (2001).