https://github.com/pcruniversum/chippcr

Toolkit of helper functions to pre-process amplification data
https://github.com/pcruniversum/chippcr

Last synced: about 1 month ago
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Toolkit of helper functions to pre-process amplification data

• Host: GitHub
• URL: https://github.com/pcruniversum/chippcr
• Owner: PCRuniversum
• Created: 2014-04-29T15:22:30.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2021-02-27T20:21:20.000Z (almost 4 years ago)
• Last Synced: 2024-11-28T22:41:38.450Z (about 1 month ago)
• Language: R
• Size: 9.07 MB
• Stars: 8
• Watchers: 4
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG

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README

        
[![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btv205)

[![R-CMD-check](https://github.com/PCRuniversum/chipPCR/workflows/R-CMD-check/badge.svg)](https://github.com/PCRuniversum/chipPCR/actions)

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.

Installation

------------

chipPCR is available [on CRAN](https://CRAN.R-project.org/package=chipPCR), so installation is as simple as:

```

install.packages("chipPCR")

```

You can install the latest development version of the code directly from GitHub:

```

source("https://install-github.me/michbur/chipPCR")

```