| Name | Description | Access |
|---|---|---|
| miRNAs and Novel miRNAs (isomiRs) | Our work on miRNAs and isomiRs includes binding site target prediction (RNA22), novel isomiRs, a mapping tool (isomiRmap), and several profiles, coordinates, sequences, and RNA22 predictions for many popular datasets. | |
| License Plates | The “License Plates” codes provide a sequence-derived nomenclature for short RNA. | |
| Mitochondrial and Nuclear tRNA fragments | The MINT project offers a comprehensive tRNA fragment (tRF) analysis kit. Discover the tRFs in your dataset (or download tRF profiles of the datasets we analyzed) and their significance in the literature using the links. | |
| Mitochondrial and Nuclear tRNA Lookalikes | Loci of the genome that resemble known mitochondrial and nuclear tRNAs. | |
| Mitochondrial and Nuclear rRNA fragments | The MINR project offers a comprehensive rRNA fragment (rRF) analysis kit. Discover the rRFs in your dataset (or download rRF profiles of the datasets we analyzed) and their significance in the literature using the links. | |
| Off-Spotter | Off-Spotter is a tool that when presented with a candidate gRNA and a PAM, quickly and exhaustively identifies all genomic sites that are identical or nearly-identical to the gRNA and also satisfy the PAM constraint. Read More. | |
| Teiresias | Teiresias ia a combinatorial algorithm for the discovery of rigid patterns (motifs) in biological sequences. Read More. | |
| Threshold-seq | R implementation of Threshold-seq, a computational method of determining thresholds for short RNA-seq datasets. | |
| Pyknons | A list of human and mouse pyknons with standardized nomenclature and a complete list of their genomics coordinates as described in this publication. | |
| Platelets | Access the data described in this 2014 publication and this 2012 publication. | |
| CLIPSim-MC | Access the data described in this publication. | |
| Small RNA mouse datasets | Next-gen datasets (gzipped tarball) mentioned in this publication. | |
| “Better Primer” | A tool to help you design better primers. | |
| Mirror of the UCSC Genome Browser | Local installation of the very popular UCSC Genome Browser allows fast browsing, secure communication, etc. |
*available only inside the TJU firewall