rtpcr: qPCR Data Analysis
Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, ${\Delta\Delta C_t}$ method) or relative expression (RE, ${\Delta C_t}$ method). The functions further provide standard errors and confidence intervals for means, apply statistical mean comparisons and present significance. To facilitate function application, different data sets were used as examples and the outputs were explained. An outstanding feature of ‘rtpcr’ package is providing publication-ready bar plots with various controlling arguments which are further editable by ggplot2 functions. The 'rtpcr' package is user-friendly and easy to work with and provides an applicable resource for analyzing real-time PCR data.
| Version: |
1.0.6 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
agricolae, ggplot2, lmerTest, purrr, reshape2, tidyr, dplyr, grid, emmeans |
| Suggests: |
knitr, rmarkdown |
| Published: |
2024-04-29 |
| Author: |
Ghader Mirzaghaderi [aut, cre, cph] |
| Maintainer: |
Ghader Mirzaghaderi <gh.mirzaghaderi at uok.ac.ir> |
| License: |
GPL-3 |
| URL: |
https://github.com/mirzaghaderi/rtpcr |
| NeedsCompilation: |
yes |
| CRAN checks: |
rtpcr results |
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