tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data

Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking. We develop...

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Bibliographic Details
Published in:BMC bioinformatics 2022-05, Vol.23 (1), p.155-155, Article 155
Main Authors: Lee, Jin-Ok, Chu, Jiyon, Jang, Gyuyeon, Lee, Minho, Chung, Yeun-Jun
Format: Article
Language:English
Subjects:
Amino acids
Base Sequence
Cell growth
Gene expression
Gene sequencing
Genomes
Graphical user interface
GUI R packages
Health aspects
Isoacceptors
Mapping
Open source software
Quality control
RNA
RNA sequencing
RNA, Transfer - genetics
Sequence Analysis, RNA
Small RNA sequence
Software
Software packages
Statistical analysis
Technology application
Transfer RNA
tRNA
tRNA expression analysis
User interface
Visualization
Workflow
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Summary:Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking. We developed a user-friendly tool, tRNA Expression Analysis Software Utilizing R for Easy use (tReasure), to analyze differentially expressed tRNAs (DEtRNAs) from deep sequencing data of small RNAs using R packages. tReasure can quantify individual mature tRNAs, isodecoders, and isoacceptors. By adopting stringent mapping strategies, tReasure supports the precise measurement of mature tRNA read counts. The whole analysis workflow for determining DEtRNAs (uploading FASTQ files, removing adapter sequences and poor-quality reads, mapping and quantifying tRNAs, filtering out low count tRNAs, determining DEtRNAs, and visualizing statistical analysis) can be performed with the tReasure package. tReasure is an open-source software available for download at https://treasure.pmrc.re.kr and will be indispensable for users who have little experience with command-line software to explore the biological implication of tRNA expression.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-022-04691-1