Package for easy and fast qPCR analysis made especially for data obtained with Viia 7 Real-time PCR system.
Install these packages in Rstudio:
install.packages(c("devtools", "tidyverse"))
Installation of qPCR package
devtools::install_github("SCIL-leuven/qPCR")
Make sure all files are .xlsx files because read_excel has problems with importing .xls files.
Import all the raw data as an excel file without any selections. We are only interested in the results, that is the third sheet. In the basic template on the Viia7, genes are Targets and samples Samples. You can find them under the Sample Name and Target Name column.
Well | Well Position | Sample Name | Target Name | CT -----|---------------|-------------|-------------|---- 1 | A1 | Sample 1 | Gene 1 | 21.23 2 | A2 | Sample 2 | Gene 1 | 24.48 3 | A3 | Sample 1 | Gene 2 | 18.98
To plot groups, you need to create an annotation file (this is the easiest to do in excel but it can also be a .csv or .txt file). Here is an example of how it should look:
Sample Name | Condition | Mouse | ... ----------|-----------|-----------|------ Sample 1 | healthy | a | ... Sample 2 | healthy | b | ... Sample 3 | diseased | a | ...
To check the example analyses run this code in the terminal:
devtools::build_vignettes()
You can also run the code chunk by chunk with Rmarkdown. Open an .Rmd file in the folder vignettes and run the chunks by pressing on the green play button top right.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.