Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data

被引：44

作者：

Akhmedov, Murodzhon ^{[1
,2
,3
]}

Martinelli, Axel ^{[1
,3
]}

Geiger, Roger ^{[1
]}

Kwee, Ivo ^{[1
,3
]}

机构：

[1] Univ Svizzera Italiana, Fac Biomed Sci, Inst Res Biomed, CH-6500 Bellinzona, Switzerland

[2] Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[3] BigOmics Analyt, CH-6500 Bellinzona, Switzerland

来源：

NAR GENOMICS AND BIOINFORMATICS | 2020年 / 2卷 / 01期

关键词：

ISOFORM SWITCHES; SIGNATURES; PROTEOME; PACKAGE; GENES;

D O I：

10.1093/nargab/lqz019

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

As the cost of sequencing drops rapidly, the amount of 'omics data increases exponentially, making data visualization and interpretation-'tertiary' analysis a bottleneck. Specialized analytical tools requiring technical expertise are available. However, consolidated and multi-faceted tools that are easy to use for life scientists is highly needed and currently lacking. Here we present Omics Playground, a user-friendly and interactive self-service bioinformatics platform for the in-depth analysis, visualization and interpretation of transcriptomics and proteomics data. It provides a large number of different tools in which special attention has been paid to single cell data. With Omics Playground, life scientists can easily perform complex data analysis and visualization without coding, and significantly reduce the time to discovery.

引用

页数：10

共 51 条

[1] Near-optimal probabilistic RNA-seq quantification (vol 34, pg 525, 2016) [J].

Bray, Nicolas L. ;

Pimentel, Harold ;

Melsted, Pall ;

Pachter, Lior .

NATURE BIOTECHNOLOGY, 2016, 34 (08) :888-888

[2]

Breiman L., 2001, IEEE Trans. Broadcast., V45, P5

[3]

Candes E, 2007, ANN STAT, V35, P2313, DOI 10.1214/009053606000001523

[4]

Chang W., 2015, PACKAGE SHINY

[5] XGBoost: A Scalable Tree Boosting System [J].

Chen, Tianqi ;

Guestrin, Carlos .

KDD'16: PROCEEDINGS OF THE 22ND ACM SIGKDD INTERNATIONAL CONFERENCE ON KNOWLEDGE DISCOVERY AND DATA MINING, 2016, :785-794

[6]

Clough E, 2016, METHODS MOL BIOL, V1418, P93, DOI 10.1007/978-1-4939-3578-9_5

[7] STAR: ultrafast universal RNA-seq aligner [J].

Dobin, Alexander ;

Davis, Carrie A. ;

Schlesinger, Felix ;

Drenkow, Jorg ;

Zaleski, Chris ;

Jha, Sonali ;

Batut, Philippe ;

Chaisson, Mark ;

Gingeras, Thomas R. .

BIOINFORMATICS, 2013, 29 (01) :15-21

[8] On the interpretation of x(2) from contingency tables, and the calculation of P [J].

Fisher, RA .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY, 1922, 85 :87-94

[9] Regularization Paths for Generalized Linear Models via Coordinate Descent [J].

Friedman, Jerome ;

Hastie, Trevor ;

Tibshirani, Rob .

JOURNAL OF STATISTICAL SOFTWARE, 2010, 33 (01) :1-22

[10] ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data [J].

Gardeux, Vincent ;

David, Fabrice P. A. ;

Shajkofci, Adrian ;

Schwalie, Petra C. ;

Deplancke, Bart .

BIOINFORMATICS, 2017, 33 (19) :3123-3125

← 1 2 3 4 5 6 →