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

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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.

Author
Le Pape Sylvain
Date of publication
None
Maintainer
Le Pape Sylvain <sylvain.le.pape@univ-poitiers.fr>
License
GPL (>=2)
Version
1.16.0

View on Bioconductor

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...

Files in this package

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