The Halushka Laboratory has worked with Drs. Alexander Baras, Toby Cornish and Matthew McCall to create useful software to characterize expression of microRNAs and proteins.  Here are links to the tools:

Find much of our code at GitHub.

  • Tracks for cell specific microRNA expression for the UCSC Genome Browser

  • Cellular microRNAome BioConductor package for R
    • You can find it here.
  • HPASubC – HPASubC allows for rapid step-through analysis of the Human Protein Atlas image bank of protein expression.  The tool can be found here:


  • miRge – miRge is an ultrafast, accurate, and local platform for microRNA alignment from high throughput small RNA-seq. The tool can be found here.


  • miRge 2.0 – This is our second version of miRge with multiple new and improved features including a novel miRNA alignment tool that is more specific that other tools out there.  The tool can be found here: