Yuk Yee Leung
DASHR - Database of small human noncoding RNA
[Source code: DASHR] The DASHR database provides information about small non-coding RNA (sncRNA) and their expression in different human tissues and cell types. The content of this database derives from curation, annotation, and computational analysis of small RNA sequencing data sets from multiple sources. Currently the database contains information about more than 46,000 sncRNAs in 42 normal human tissues and cell types from over 30 independent studies. This work is described in Leung et al. (Nucleic Acids Research Database Issue, 2016). The DASHR database and complete instructions can be found here.
CoRAL - Classification of RNAs by Analysis of Length
[Source code: CoRAL] CoRAL is a machine learning tool / package that can predict the precursor class of small noncoding RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are the most important for discriminating different populations of small non-coding RNAs. This work is described in Leung et al. (Nucleic Acids Research, 2013). Complete instructions and documentation can be found here.
HAMR - High throughput Annotation of Modified Ribonucleotides
[Source code: HAMR] HAMR (High-throughput Annotation of Modified Ribonucleotides) is a web application that allows you to detect and classify modified nucleotides in RNA-seq data. HAMR scans RNA-sequencing data for sites showing potential signatures of nucleotide modification. Users can input particular genomic regions of interest (BED file format) and HAMR will output a table containing the list of sites with nucleotide patterns that deviate from expectation at a statistically significant rate. This work is described in Ryvkin et al. (RNA, 2013). The webserver and complete instructions can be found here.