Software

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:

  • 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: https://github.com/cornish/HPASubC.

HPASubC

  • miRge – miRge is an ultrafast, accurate, and local platform for microRNA alignment from high throughput small RNA-seq. The tool can be found here: http://atlas.pathology.jhu.edu/baras/miRge.html.  Stay tuned for miRge 2.0, in production now.

miRge

mirqc_expr