RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.
Cloud deployment
Differential expression analysis
Docker
Pathway analysis
Pipeline
RNA-seq
Stand-alone software
ncRNAs
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
03 Jun 2021
03 Jun 2021
Historique:
received:
08
11
2020
accepted:
20
05
2021
entrez:
4
6
2021
pubmed:
5
6
2021
medline:
8
6
2021
Statut:
epublish
Résumé
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.
Sections du résumé
BACKGROUND
BACKGROUND
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.
RESULTS
RESULTS
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.
CONCLUSIONS
CONCLUSIONS
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.
Identifiants
pubmed: 34082707
doi: 10.1186/s12859-021-04211-7
pii: 10.1186/s12859-021-04211-7
pmc: PMC8173825
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
298Subventions
Organisme : Ministero dell'Istruzione, dell'Università e della Ricerca
ID : B96G18000590005
Organisme : PO-FESR Sicilia 14-20
ID : G89J18000700007
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