CRAN/E | chipPCR

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

Installation

About

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) doi:10.1093/bioinformatics/btv205.

Citation chipPCR citation info
github.com/PCRuniversum/chipPCR
Bug report File report

Key Metrics

Version 1.0-2
R ≥ 3.0.0
Published 2021-03-05 1119 days ago
Needs compilation? no
License GPL-3
CRAN checks chipPCR results
Language en-US

Downloads

Yesterday 27 +170%
Last 7 days 202 +13%
Last 30 days 865 -8%
Last 90 days 2.750 +24%
Last 365 days 10.070 +1%

Maintainer

Maintainer

Stefan Roediger

stefan.roediger@b-tu.de

Authors

Stefan Roediger

cre / aut

Michal Burdukiewicz

aut

Konstantin A. Blagodatskikh

ctb

Andrej-Nikolai Spiess

ctb

Material

README
NEWS
ChangeLog
Reference manual
Package source

Vignettes

Supplement to: chipPCR: an R Package to Pre-Process Raw Data of Amplification Curves

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

chipPCR archive

Depends

R ≥ 3.0.0
methods

Imports

lmtest
MASS
outliers
ptw
quantreg
Rfit
robustbase
shiny
signal

Suggests

drc
knitr
markdown
qpcR
RDML
rmarkdown
spelling
testthat
tinytex
xtable

Reverse Imports

MBmca
PCRedux

Reverse Suggests

RDML
shinyMolBio