NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization

Background As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skil...

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Vydané v:BMC bioinformatics Ročník 21; číslo 1; s. 1 - 14
Hlavní autori: Yousif, Ayman, Drou, Nizar, Rowe, Jillian, Khalfan, Mohammed, Gunsalus, Kristin C.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 29.06.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Applications programs
Binding sites
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Data analysis
Data processing
Exploratory data analysis
Gene expression
Genetic engineering
Graphical user interface
Interactive visualization
Internet software
Life Sciences
Metagenomics
Microarrays
Next-generation sequencing
Nucleic acids
Open source software
Personal computers
Privacy
Researchers
Ribonucleic acid
RNA
Sequence analysis
Software
Software development tools
Software packages
Source code
Transcriptomics
Usability
User interface
Visualization
Visualization (Computer)
Web applications
Interactive visualization
Transcriptomics
Exploratory data analysis
Graphical user interface
ISSN:1471-2105, 1471-2105
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Shrnutí:Background As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource). Results NASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/ . Open-source code is on GitHub at https://github.com/nasqar/NASQAR , and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall . NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology. Conclusions NASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-020-03577-4