BiasCorrector

BiasCorrector is the user friendly implementation of the algorithms described by Moskalev et. al in their research article 'Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression', published 2011 in Nucleic acids research, Oxford University Press (DOI: https://doi.org/10.1093/nar/gkr213).

Installation

Using R

• Make sure, you have R installed on your system:

  • https://cran.r-project.org/

• Then open your development environment and install this R package:

CRAN version

You can install BiasCorrector simply with via R's install.packages interface:

install.packages("BiasCorrector")

development version

If you want to use the latest development version, you can install the github version of BiasCorrector with:

install.packages("devtools")
devtools::install_github("kapsner/BiasCorrector")

• To start BiasCorrector, just run the following command in R. A browser tab should open displaying BiasCorrector. Alternatively you can type the URL "localhost:3838/" in your browser.

library(BiasCorrector)
launch_app()

Using Docker

To simplify installation an deployment of BiasCorrector you can clone this repository and build your own docker image. Make sure, you have Docker and docker-compose installed on your system.

Build Docker Image Manually

# clone the repository
git clone https://github.com/kapsner/BiasCorrector

# go to the docker subfolder
cd BiasCorrector/docker/

# run the build script
./build_image.sh

# when the building is finished, just start the container by running
docker-compose -f docker-compose.local.yml up -d

Using a Remote Docker Image

# clone the repository
git clone https://github.com/kapsner/BiasCorrector

# go to the docker subfolder
cd BiasCorrector/docker/

# start the Docker container
docker-compose -f docker-compose.remote.yml up -d

Type the URL "localhost:3838/" in your browser and start working with BiasCorrector.

rBiasCorrection

BiasCorrector depends on the rBiasCorrection R-package, which is the implementation of the core functionality to correct measurement biases in DNA methylation analyses. BiasCorrector brings this functionality to a user-friendly shiny web application.
rBiasCorrection is available at https://github.com/kapsner/rBiasCorrection.

Video Tutorial

A video tutorial describing the workflow of how to use BiasCorrector in order to correct measurement bias in DNA methylation data is available on youtube.

Demo Version

A demo version of BiasCorrector is available here.

Frequently Asked Questions

FAQs can be found here.

Citation

@article{10.1093/nar/gkr213,
    author = {Moskalev, Evgeny A. and Zavgorodnij, Mikhail G. and Majorova, Svetlana P. and Vorobjev, Ivan A. and Jandaghi, Pouria and Bure, Irina V. and Hoheisel, Jörg D.},
    title = "{Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression}",
    journal = {Nucleic Acids Research},
    volume = {39},
    number = {11},
    pages = {e77-e77},
    year = {2011},
    month = {04},
    issn = {0305-1048},
    doi = {10.1093/nar/gkr213},
    url = {https://dx.doi.org/10.1093/nar/gkr213},
    eprint = {http://oup.prod.sis.lan/nar/article-pdf/39/11/e77/16775711/gkr213.pdf},
}

More Infos

• Original work by Moskalev et al.: https://doi.org/10.1093/nar/gkr213
• about RStudio: https://www.rstudio.com/products/rstudio/
• about Shiny: https://www.rstudio.com/products/shiny/
• about Shiny Server: https://www.rstudio.com/products/shiny/shiny-server/
• RStudio and Shiny are trademarks of RStudio, Inc.
• about Docker: https://www.docker.com/