---
title: "Microbead Surface Nucleic Acid Melting Curve Analysis"
author: "The MBmca package authors"
date: "`r Sys.Date()`"
output: 
  rmarkdown::pdf_document:
    number_sections: true
    toc: true
    toc_depth: 3
header-includes:
    - \usepackage[font={small}]{caption}
bibliography: "MBmca.bib"
vignette: >
  %\VignetteIndexEntry{Supplement to: Microbead Surface Nucleic Acid Melting Curve Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

The MBmca package was developed for the analysis of melt curve data. 
Specifically, algorithms were developed for the analysis of the melting behavior 
of nucleic acid hybrids on the surface of microbeads.

However, the software is also useful for the analysis of data from melting 
curves of qPCRs. The \emph{diffQ2()} function approximately calculates the 
maximum and minimum of the second derivative. These values can also be used as 
quantification points. For example, the maximum of the second derivative is a 
frequently used parameter in determining the Cq value of qPCRs. A further 
application can be the analysis of data from opaque isothermal amplifications.

Details on the application of the software are in the publications

- @roediger_RJ_2013
- @rodiger_r_2015

described.

The software has been lost in conjunction with the VideoScan platform. This is a 
fully automatic multispectral fluorescence microscope for the multiplex analysis 
of biomarkers [@roediger_highly_2013]. Applications of the platform can be found 
in personalized medicine and life sciences [@rodiger_nucleic_2014; @willitzki_new_2012].

Over the years, a lot of knowledge has accumulated on the analysis of data from 
quantitative PCRs and melting curves. Thus, we could show that the use of 
filters and smoothing functions affect the parameter estimation of amplification 
curves [@spiess_impact_2014]. The MBmca package also applies filters and smoothing functions to melt 
curves. This should be taken into account when using the software.

# References
