Software Scripts and console applications miRPCR

miRPCR

Author: Roman Jaksik

miRPCR can be used to standardize RT-qPCR results obtained for various miRNAs using snRNA/snoRNA as a reference, test for statistical significance between various conditions and to visualize the results.

Usage:

library('mirPCR')

mirPCR(data_file, control_rna, reference_factor, plot_file_name = NULL, ctrl_div = FALSE)

 

The required parameters include:

  • data_file - table saved in a tab-delimited text file, which should include the following columns:
    • Gene - miRNA symbol or any other identifier e.g hsa-miR-21a
    • Factor - factors which will be compared e.g. Normal, Tumor
    • Patient - IDs of individual patients/cell lines
    • Ct - cycle threshold value obtained in the RT-qPCR experiment
  • control_rna - symbol of the control RNA e.g. SNORD-75 (this ID has to be included in the data table)
  • reference_factor - factor to be used as a reference in the statistical tests e.g Normal (this factor has to be included in the data table)
  • plot_file_name - resulting plot file name (without extension), if not provided the plot will not be saved to a file (default: NULL)
  • ctrl_div - if TRUE divide the measurements by the average control signal (default: FALSE) 

 

Installation:

install.packages("mirPCR.tar.gz", repos = NULL, type = "source")

 

 

R package binary: