SCANPY: large-scale single-cell gene expression data analysis

被引：3647

作者：

Wolf, F. Alexander ^{[1
]}

Angerer, Philipp ^{[1
]}

Theis, Fabian J. ^{[1
,2
]}

机构：

[1] Helmholtz Zentrum Munchen, German Res Ctr Environm Hlth, Inst Computat Biol, Munich, Germany

[2] Tech Univ Munich, Dept Math, Munich, Germany

来源：

GENOME BIOLOGY | 2018年 / 19卷

关键词：

Single-cell transcriptomics; Machine learning; Scalability; Graph analysis; Clustering; Pseudotemporal ordering; Trajectory inference; Differential expression testing; Visualization; Bioinformatics; HETEROGENEITY; RECONSTRUCTION; VISUALIZATION;

D O I：

10.1186/s13059-017-1382-0

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (https://github.com/theislab/Scanpy). Along with SCANPY, we present ANNDATA, a generic class for handling annotated data matrices (https://github.com/theislab/anndata).

引用

页数：5

共 52 条

[21] Diffusion pseudotime robustly reconstructs lineage branching [J].

Haghverdi, Laleh ;

Buettner, Maren ;

Wolf, F. Alexander ;

Buettner, Florian ;

Theis, Fabian J. .

NATURE METHODS, 2016, 13 (10) :845-+

[22] Diffusion maps for high-dimensional single-cell analysis of differentiation data [J].

Haghverdi, Laleh ;

Buettner, Florian ;

Theis, Fabian J. .

BIOINFORMATICS, 2015, 31 (18) :2989-2998

[23]

Huber W, 2015, NAT METHODS, V12, P115, DOI [10.1038/NMETH.3252, 10.1038/nmeth.3252]

[24] Matplotlib: A 2D graphics environment [J].

Hunter, John D. .

COMPUTING IN SCIENCE & ENGINEERING, 2007, 9 (03) :90-95

[25]

Kharchenko PV, 2014, NAT METHODS, V11, P740, DOI [10.1038/nmeth.2967, 10.1038/NMETH.2967]

[26] Deep learning [J].

LeCun, Yann ;

Bengio, Yoshua ;

Hinton, Geoffrey .

NATURE, 2015, 521 (7553) :436-444

[27] Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis [J].

Levine, Jacob H. ;

Simonds, Erin F. ;

Bendall, Sean C. ;

Davis, Kara L. ;

Amir, El-ad D. ;

Tadmor, Michelle D. ;

Litvin, Oren ;

Fienberg, Harris G. ;

Jager, Astraea ;

Zunder, Eli R. ;

Finck, Rachel ;

Gedman, Amanda L. ;

Radtke, Ina ;

Downing, James R. ;

Pe'er, Dana ;

Nolan, Garry P. .

CELL, 2015, 162 (01) :184-197

[28]

Lippert C., 2014, LIMIX GENETIC ANAL M

[29]

Lun Aaron T L, 2016, F1000Res, V5, P2122

[30]

Lun ATL, 2017, BIORXIV

← 1 2 3 4 5 6 →