EasyqpcR: EasyqpcR for low-throughput real-time quantitative PCR data analysis
Version 1.18.0

This package is based on the qBase algorithms published by Hellemans et al. in 2007. The EasyqpcR package allows you to import easily qPCR data files as described in the vignette. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. This package has been created for low-throughput qPCR data analysis.

AuthorLe Pape Sylvain
Bioconductor views GeneExpression qPCR
Date of publicationNone
MaintainerLe Pape Sylvain <sylvain.le.pape@univ-poitiers.fr>
LicenseGPL (>=2)
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EasyqpcR")

Getting started

Package overview

Popular man pages

badCt: Evaluation of the qPCR technical replicates
EasyqpcR-package: Functions to analyse real-time quantitative PCR data at...
Efficiency_calculation: Raw data for primer amplification efficiency calculation.
nrmData: Determination of the NF, RQ, NRQ, NRQ scaled to control and...
qPCR_run2: Raw data from the second qPCR run.
slope: Function to calculate the amplification efficiency
totData: Aggregation of qPCR biological replicates and data...
See all...

All man pages Function index File listing

Man pages

badCt: Evaluation of the qPCR technical replicates
calData: Calculation of calibration factors
EasyqpcR-package: Functions to analyse real-time quantitative PCR data at...
Efficiency_calculation: Raw data for primer amplification efficiency calculation.
Gene_maximisation: A data frame containing all the data from four different qPCR...
Gene_maximisation_cor: A data frame containing all the data from four different qPCR...
nrmData: Determination of the NF, RQ, NRQ, NRQ scaled to control and...
qPCR_run1: Raw data from the first qPCR run.
qPCR_run2: Raw data from the second qPCR run.
qPCR_run3: Raw data from the third qPCR run.
slope: Function to calculate the amplification efficiency
totData: Aggregation of qPCR biological replicates and data...

Functions

EasyqpcR Man page
EasyqpcR-package Man page
Efficiency_calculation Man page
Gene_maximisation Man page
Gene_maximisation_cor Man page
badCt Man page Source code
calData Man page Source code
nrmData Man page Source code
qPCR_run1 Man page
qPCR_run2 Man page
qPCR_run3 Man page
slope Man page Source code
totData Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/badCt.R
R/calData.R
R/nrmData.R
R/slope.R
R/totData.R
build
build/vignette.rds
data
data/Efficiency_calculation.rda
data/Gene_maximisation.csv.gz
data/Gene_maximisation.rda
data/Gene_maximisation_cor.csv.gz
data/Gene_maximisation_cor.rda
data/qPCR_run1.csv.gz
data/qPCR_run1.rda
data/qPCR_run2.rda
data/qPCR_run3.rda
inst
inst/CITATION
inst/doc
inst/doc/vignette_EasyqpcR.R
inst/doc/vignette_EasyqpcR.Rnw
inst/doc/vignette_EasyqpcR.pdf
inst/extdata
inst/extdata/Gene_maximisation.csv
inst/extdata/Gene_maximisation_cor.csv
inst/extdata/qPCR_run1.csv
man
man/EasyqpcR-package.Rd
man/Efficiency_calculation.Rd
man/Gene_maximisation.Rd
man/Gene_maximisation_cor.Rd
man/badCt.Rd
man/calData.Rd
man/nrmData.Rd
man/qPCR_run1.Rd
man/qPCR_run2.Rd
man/qPCR_run3.Rd
man/slope.Rd
man/totData.Rd
vignettes
vignettes/.install_extras
vignettes/Gene_max.jpg
vignettes/Gene_max2.jpg
vignettes/Gene_max3.jpg
vignettes/Makefile
vignettes/Sample_max.png
vignettes/dataimport.png
vignettes/dataimport2.png
vignettes/logoirtomit.jpg
vignettes/vignette_EasyqpcR.Rnw
vignettes/vignette_EasyqpcR.brf
vignettes/vignette_EasyqpcR.toc
EasyqpcR documentation built on May 20, 2017, 9:41 p.m.