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

被引：464

作者：

Kiselev, Vladimir Yu ^{[1
]}

Yiu, Andrew ^{[1
]}

Hemberg, Martin ^{[1
]}

机构：

[1] Wellcome Sanger Inst, Hinxton, England

来源：

NATURE METHODS | 2018年 / 15卷 / 05期

基金：

英国惠康基金;

关键词：

EXPRESSION; MOUSE;

D O I：

10.1038/nmeth.4644

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

收藏

页码：359 / +

页数：6

相关论文

共 30 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2]

Andrews TS, 2016, BIORXIV

[3] A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure [J].

Baron, Maayan ;

Veres, Adrian ;

Wolock, Samuel L. ;

Faust, Aubrey L. ;

Gaujoux, Renaud ;

Vetere, Amedeo ;

Ryu, Jennifer Hyoje ;

Wagner, Bridget K. ;

Shen-Orr, Shai S. ;

Klein, Allon M. ;

Melton, Douglas A. ;

Yanai, Itai .

CELL SYSTEMS, 2016, 3 (04) :346-+

[4] Support vector clustering [J].

Ben-Hur, A ;

Horn, D ;

Siegelmann, HT ;

Vapnik, V .

JOURNAL OF MACHINE LEARNING RESEARCH, 2002, 2 (02) :125-137

[5] Random forests [J].

Breiman, L .

MACHINE LEARNING, 2001, 45 (01) :5-32

[6]

Brennecke P, 2013, NAT METHODS, V10, P1093, DOI [10.1038/nmeth.2645, 10.1038/NMETH.2645]

[7]

Butler A., 2017, bioRxiv

[8] Multilineage communication regulates human liver bud development from pluripotency [J].

Camp, J. Gray ;

Sekine, Keisuke ;

Gerber, Tobias ;

Loeffler-Wirth, Henry ;

Binder, Hans ;

Gac, Malgorzata ;

Kanton, Sabina ;

Kageyama, Jorge ;

Damm, Georg ;

Seehofer, Daniel ;

Belicova, Lenka ;

Bickle, Marc ;

Barsacchi, Rico ;

Okuda, Ryo ;

Yoshizawa, Emi ;

Kimura, Masaki ;

Ayabe, Hiroaki ;

Taniguchi, Hideki ;

Takebe, Takanori ;

Treutlein, Barbara .

NATURE, 2017, 546 (7659) :533-+

[9] WEIGHTED KAPPA - NOMINAL SCALE AGREEMENT WITH PROVISION FOR SCALED DISAGREEMENT OR PARTIAL CREDIT [J].

COHEN, J .

PSYCHOLOGICAL BULLETIN, 1968, 70 (04) :213-&

[10] Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor [J].

Crow, Megan ;

Paul, Anirban ;

Ballouz, Sara ;

Huang, Z. Josh ;

Gillis, Jesse .

NATURE COMMUNICATIONS, 2018, 9