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Plea for PCRuniversum

Plea for pcRuniveRsum - R qPCR / dPCR / MCA Landscape

Read on Stefan’s homepage.

Packages in pcRuniveRsum (in alphabetical order)

chipPCR

Changelog of the stable version

The chipPCR package is a toolkit of functions to preprocess amplification curve data. Amplification data can be obtained from conventional PCR reactions or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, a routine to detect the start of an amplification reaction, several smoothers for amplification data, a function to distinguish positive and negative amplification reactions and a function to determine the amplification efficiency. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others.

In addition the first approximate approximate derivative maximum (FDM) and second approximate derivative maximum (SDM) can be calculated by a 5-point-stencil as quantification points from real-time amplification curves. chipPCR contains data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR (ccPCR) system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

Web services:

AmpSim
MFIaggr

dpcR

Changelog of the stable version

dpcR provides tools for analysis, visualisation and simulation of digital PCR experiments. It contains methods of comparing dPCR reactions, convertion of qPCR experiments to dPCR and spatial randomness tests.

Web services:

dpcr_density: calculates and plots the density of the number of positive molecules or the average number of molecules per partition. test_counts: showcase for usage of Generalized Linear models for comparing digital PCR experiments.

mbMCA

Changelog of the stable version

The MBmca package provides data sets and lightweight utilities for nucleic acid melting curve analysis and presentation on microbead surfaces.

RDML

Changelog of the stable version

Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) format files and transforms to the appropriate formats of the ‘qpcR’ and ‘chipPCR’ packages.