UCSC Cell Browser: visualize your single-cell data

被引：144

作者：

Speir, Matthew L. ^{[1
]}

Bhaduri, Aparna ^{[2
]}

Markov, Nikolay S. ^{[3
]}

Moreno, Pablo ^{[4
]}

Nowakowski, Tomasz J. ^{[5
,6
,7
,8
]}

Papatheodorou, Irene ^{[4
]}

Pollen, Alex A. ^{[5
,9
]}

Raney, Brian J. ^{[1
]}

Seninge, Lucas ^{[1
,10
]}

Kent, W. James ^{[1
]}

Haeussler, Maximilian ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA

[2] Univ Calif Los Angeles, Dept Biol Chem, Los Angeles, CA 90095 USA

[3] Northwestern Univ, Feinberg Sch Med, Div Pulm & Crit Care, Chicago, IL 60611 USA

[4] EMBL EBI European Bioinformat Inst, Wellcome Genome Campus, Cambridge CB10 1SD, England

[5] Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USA

[6] Univ Calif San Francisco, Dept Anat, San Francisco, CA 94143 USA

[7] Univ Calif San Francisco, Dept Psychiat & Behav Sci, San Francisco, CA 94143 USA

[8] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA

[9] Univ Calif San Francisco, Dept Neurol, San Francisco, CA 94143 USA

[10] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

来源：

BIOINFORMATICS | 2021年 / 37卷 / 23期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/btab503

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.

引用

页码：4578 / 4580

页数：3

共 15 条

[1] The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update [J].

Afgan, Enis ;

Baker, Dannon ;

Batut, Berenice ;

van den Beek, Marius ;

Bouvier, Dave ;

Cech, Martin ;

Chilton, John ;

Clements, Dave ;

Coraor, Nate ;

Gruening, Bjoern A. ;

Guerler, Aysam ;

Hillman-Jackson, Jennifer ;

Hiltemann, Saskia ;

Jalili, Vahid ;

Rasche, Helena ;

Soranzo, Nicola ;

Goecks, Jeremy ;

Taylor, James ;

Nekrutenko, Anton ;

Blankenberg, Daniel .

NUCLEIC ACIDS RESEARCH, 2018, 46 (W1) :W537-W544

[2] Integrating single-cell transcriptomic data across different conditions, technologies, and species [J].

Butler, Andrew ;

Hoffman, Paul ;

Smibert, Peter ;

Papalexi, Efthymia ;

Satija, Rahul .

NATURE BIOTECHNOLOGY, 2018, 36 (05) :411-+

[3] Comparison of visualization tools for single-cell RNAseq data [J].

Cakir, Batuhan ;

Prete, Martin ;

Huang, Ni ;

van Dongen, Stijn ;

Pir, Pinar ;

Kiselev, Vladimir Yu .

NAR GENOMICS AND BIOINFORMATICS, 2020, 2 (03)

[4] Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects [J].

de Soysa, T. Yvanka ;

Ranade, Sanjeev S. ;

Okawa, Satoshi ;

Ravichandran, Srikanth ;

Huang, Yu ;

Salunga, Hazel T. ;

Schricker, Amelia ;

del Sol, Antonio ;

Gifford, Casey A. ;

Srivastava, Deepak .

NATURE, 2019, 572 (7767) :120-+

[5] Dimensionality reduction by UMAP to visualize physical and genetic interactions [J].

Dorrity, Michael W. ;

Saunders, Lauren M. ;

Queitsch, Christine ;

Fields, Stanley ;

Trapnell, Cole .

NATURE COMMUNICATIONS, 2020, 11 (01)

[6] Bioconda: sustainable and comprehensive software distribution for the life sciences [J].

Gruening, Bjoern ;

Dale, Ryan ;

Sjoedin, Andreas ;

Chapman, Brad A. ;

Rowe, Jillian ;

Tomkins-Tinch, Christopher H. ;

Valieris, Renan ;

Koester, Johannes ;

Team, Bioconda .

NATURE METHODS, 2018, 15 (07) :475-476

[7] Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease [J].

Kathiriya, Irfan S. ;

Rao, Kavitha S. ;

Iacono, Giovanni ;

Devine, W. Patrick ;

Blair, Andrew P. ;

Hota, Swetansu K. ;

Lai, Michael H. ;

Garay, Bayardo, I ;

Thomas, Reuben ;

Gong, Henry Z. ;

Wasson, Lauren K. ;

Goyal, Piyush ;

Sukonnik, Tatyana ;

Hu, Kevin M. ;

Akgun, Gunes A. ;

Bernard, Laure D. ;

Akerberg, Brynn N. ;

Gu, Fei ;

Li, Kai ;

Speir, Matthew L. ;

Haeussler, Maximilian ;

Pu, William T. ;

Stuart, Joshua M. ;

Seidman, Christine E. ;

Seidman, J. G. ;

Heyn, Holger ;

Bruneau, Benoit G. .

DEVELOPMENTAL CELL, 2021, 56 (03) :292-+

[8] User-friendly, scalable tools and workflows for single-cell RNA-seq analysis [J].

Moreno, Pablo ;

Huang, Ni ;

Manning, Jonathan R. ;

Mohammed, Suhaib ;

Solovyev, Andrey ;

Polanski, Krzysztof ;

Bacon, Wendi ;

Chazarra, Ruben ;

Talavera-Lopez, Carlos ;

Doyle, Maria A. ;

Marnier, Guilhem ;

Gruening, Bjoern ;

Rasche, Helena ;

George, Nancy ;

Fexova, Silvie Korena ;

Alibi, Mohamed ;

Miao, Zhichao ;

Perez-Riverol, Yasset ;

Haeussler, Maximilian ;

Brazma, Alvis ;

Teichmann, Sarah ;

Meyer, Kerstin B. ;

Papatheodorou, Irene .

NATURE METHODS, 2021, 18 (04) :327-328

[9] Expression Atlas update: from tissues to single cells [J].

Papatheodorou, Irene ;

Moreno, Pablo ;

Manning, Jonathan ;

Fuentes, Alfonso Munoz-Pomer ;

George, Nancy ;

Fexova, Silvie ;

Fonseca, Nuno A. ;

Fullgrabe, Anja ;

Green, Matthew ;

Huang, Ni ;

Huerta, Laura ;

Lqbal, Haider ;

Jianu, Monica ;

Mohammed, Suhaib ;

Zhao, Lingyun ;

Jarnuczak, Andrew F. ;

Jupp, Simon ;

Marioni, John ;

Meyer, Kerstin ;

Petryszak, Robert ;

Medina, Cesar Augusto Prada ;

Talavera-Lopez, Carlos ;

Teichmann, Sarah ;

Vizcaino, Juan Antonio ;

Brazma, Alvis .

NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D77-D83

[10] The Human Cell Atlas [J].

Regev, Aviv ;

Teichmann, Sarah A. ;

Lander, Eric S. ;

Amt, Ido ;

Benoist, Christophe ;

Birney, Ewen ;

Bodenmiller, Bernd ;

Campbell, Peter ;

Carninci, Piero ;

Clatworthy, Menna ;

Clevers, Hans ;

Deplancke, Bart ;

Dunham, Ian ;

Eberwine, James ;

Elis, Roland ;

Enard, Wolfgang ;

Farmer, Andrew ;

Fugger, Lars ;

Gottgens, Berthold ;

Hacohen, Nir ;

Haniffa, Muzlifah ;

Hemberg, Martin ;

Kim, Seung ;

Klenerman, Paul ;

Kriegstein, Arnold ;

Lein, E. D. ;

Linnarsson, Sten ;

Lundberg, Emma ;

Lundeberg, Jaokim ;

Majumder, Partha ;

Marioni, John C. ;

Merad, Miriam ;

Mhlanga, Musa ;

Nawijin, Martijn ;

Netea, Mihai ;

Nolan, Garry ;

Pe'er, Dana ;

Phillipakis, Anthony ;

Ponting, Chris P. ;

Quake, Stephen ;

Reik, Wolf ;

Rozenblatt-Rosen, Orit ;

Sanes, Joshua ;

Satija, Rahul ;

Schumacher, Ton N. ;

Shalek, Alex ;

Shapiro, Ehud ;

Sharma, Padmanee ;

Shin, Jay W. ;

Stegle, Oliver .

ELIFE, 2017, 6

← 1 2 →