pyQPCR

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 09/03/10
  • Minor correction: 11/01/12
Keywords

pyQPCR : analysis of real-time quantitative PCR data supplying relative quantifications

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows, MacOS X
  • Current version: pyqpcr-0.9 - 03/01/2012
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Thomas GASTINE, Magali HENNION
  • Contact designer(s): tgastineATusers.sourceforge.net
  • Laboratory, service: LBME

 

General software features

pyQPCR is a free software for biologists. It purpose is to analyze quantitative PCR (polymerase chain reaction) data to supply relative or absolute quantification. This method has become one of the most widely used methods of gene quantification but many users run up against troubles to convert raw data into reliable quantities with a good estimation of the errors.

From qPCR raw data (Ct or threshold cycle) imported from one or several plates (96 or 384 wells), the software calculates PCR efficiency by standard curves analysis (with the error), and relative quantification by the improved method of delta-delta Ct (Hellemans et al., 2007) or absolute quantification. A plate outline allow you to precise what sample is in each well, and then a click runs the calculations. Results are displayed in a table and plotted as graphs easy to customize.

We'd like to give to users a tool as complete as possible using recent algorithms that are widely accepted by the scientific community. The software can import raw data from different devices (Eppendorf Realplex , Applied AB7000, AB7500, AB7700, AB7900 and ABStepOne, Roche LightCycler 480, Biorad MyIQ 2 and 5, Biorad C1000, Cepheid SmartCycler, Qiagen Corbett, Stratagene Mx3000 and Mx3005, ESCO spectrum 48, Illumina Eco). The extension to others qPCR devices is easy and will be done as soon as we'll have an example of raw data file from others instruments (don't hesitate to send us your files). The software can import and analyze data from several plates in a same project. Moreover several reference genes can be used.

pyQPCR is encoded using python programming language and Qt4 library for graphics. So, it is usable on all operating systems (Linux, Windows and MacOS X).

Context in which the software is used

pyQPCR is stable and we still are developing new functionalities. Graphics are accomplished, we have sorted out the last statistical troubles and added the resource to take into account several plates and several reference genes. We are now fixing minor bugs, adding new qPCR devices and writing more complete help and tutorial. The software is still poorly distributed but we are currently working to finalize it and enlarge distribution.