RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional tech...

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Bibliographic Details
Published in:BMC bioinformatics 2021-06, Vol.22 (1), p.1-298, Article 298
Main Authors: La Ferlita, Alessandro, Alaimo, Salvatore, Di Bella, Sebastiano, Martorana, Emanuele, Laliotis, Georgios I, Bertoni, Francesco, Cascione, Luciano, Tsichlis, Philip N, Ferro, Alfredo, Bosotti, Roberta, Pulvirenti, Alfredo
Format: Article
Language:English
Subjects:
Applications software
Bioinformatics
Cloud computing
Cloud deployment
Computational biology
Computer applications
Computer graphics
Computer programs
Data analysis
Docker
Gene expression
Genomes
Graphical user interface
Laboratories
Methods
ncRNAs
Non-coding RNA
Operating systems
Outsourcing
Pipeline
RNA sequencing
RNA-seq
Servers
Software
Stand-alone software
Technology
Transcriptomes
User interface
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Summary:RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04211-7