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sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression

2019 Nucleic Acids Research  
These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers.  ...  Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing  ...  In 2015, we introduced sRNAtoolbox (9), a collection of small RNA research tools built around sRN-Abench, providing different downstream analysis including consensus differential expression, target prediction  ... 
doi:10.1093/nar/gkz415 pmid:31114926 pmcid:PMC6602500 fatcat:pzqld3qrmjfkxbe3tgfnmzcixy

miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline [article]

Arun H Patil, Marc K. Halushka
2021 bioRxiv   pre-print
MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes.  ...  tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench.  ...  ACKNOWLEDGEMENTS The authors thank the Pathology Department IT department for providing a Mac computer for the developing and testing of miRge3.0 GUI on Mac OS (OS-X) and the use of the Ares Linux server  ... 
doi:10.1101/2021.01.18.427129 fatcat:gylwbvxpqfdvhaz4wzprbtdrnq

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA [article]

Ting Zhang, Jingjing Zhai, Xiaorong Zhang, Lei Ling, Menghan Li, Shang Xie, Minggui Song, Chuang Ma
2020 bioRxiv   pre-print
The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools.  ...  MicroRNAs (miRNAs) are important regulators of gene expression.  ...  All authors read and approved the final manuscript. . sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential 433 expression.  ... 
doi:10.1101/2020.12.01.405399 fatcat:sdxm4mjom5h5lnzao2zjotuku4