ProntoPCR

ProntoPCR is a user-friendly and efficient R Shiny application designed for real-time PCR (qPCR) or reverse transcriptase qPCR (RT-qPCR) data analysis. It automates calculations such as averaging housekeeper genes, Cq, Cq, 2^-Cq, 2^-Cq, making it easy to analyse gene expression data.

How It Works

1. Upload Data: Import your qPCR data (Cq means, Target, Samples) in CSV format.
2. Set Parameters: Select housekeeping genes and/or control groups + target genes.
3. Analyse: ProntoPCR calculates key metrics automatically. Users can download results as a CSV file.
4. Statistics: Select and perform desired statistics on calculated data. Users can download statistic results as a HTML file.
5. Visualise: Customise and download publication-ready graphs directly from the app.

Availability

ProntoPCR has been designed to operate both online and locally. Whilst we aim to maintain online availability, the hosted platform may change or become unavailable. Therefore, it is recommended to rely on the local version, which functions with the same features as the online option. The local version also does not require internet access once installed. To run the application locally, the user needs to download R and RStudio.

Local Installation

For detailed installation instructions, especially for users unfamilar with the R coding language, refer to the ProntoPCR Handbook.

To use ProntoPCR, you can install it directly from GitHub within the R console:

```r

Install devtools package if not already installed

install.packages("devtools")

Load devtools library within R session

library(devtools)

Install ProntoPCR from GitHub

devtools::install_github("MarnieMaddock/ProntoPCR")

Run the application

library(ProntoPCR) ProntoPCR() ```

MacOS or Restricted-Network Users

For some macOS or restricted network users, the above installation instructions may fail. To fix this, you can force the curl download method by running the following code in your R console:

```r

Install devtools package if not already installed

install.packages("devtools")

Set download options

options(download.file.method = "curl")

Install ProntoPCR from GitHub

devtools::install_github("MarnieMaddock/ProntoPCR")

Run the application

library(ProntoPCR) ProntoPCR()

```

Online Access

ProntoPCR Online

Instuctions for Use

How to use instructions are available within the ProntoPCR Handbook.

Citation

If ProntoPCR is used for your analysis, please cite the journal article:

Feedback and Support

If you encounter any issues or have suggestions, feel free to:

• Open an issue on this repository
• Email Us

Contributions

We welcome contributions. If you'd like to contribute, please:

• Fork this repository.
• Create a new branch for your feature or bug fix.
• Submit a pull request with a detailed explanation of your changes.

License

ProntoPCR is licensed under the MIT License. See LICENSE for details.