https://github.com/kapsner/biascorrector
R package providing a shiny GUI to the functions implemented in rBiasCorrection
https://github.com/kapsner/biascorrector
bias-correction cran gene-methylation genetics gui pcr r r-package shiny
Last synced: 17 days ago
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R package providing a shiny GUI to the functions implemented in rBiasCorrection
- Host: GitHub
- URL: https://github.com/kapsner/biascorrector
- Owner: kapsner
- License: gpl-3.0
- Created: 2018-11-25T15:46:38.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-10-17T15:17:41.000Z (7 months ago)
- Last Synced: 2024-10-19T18:32:32.089Z (7 months ago)
- Topics: bias-correction, cran, gene-methylation, genetics, gui, pcr, r, r-package, shiny
- Language: R
- Homepage:
- Size: 526 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
Awesome Lists containing this project
README
# BiasCorrector
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://cran.r-project.org/package=BiasCorrector)
[](https://cran.r-project.org/web/checks/check_results_BiasCorrector.html)
[](https://cran.r-project.org/package=BiasCorrector)
[](https://cran.r-project.org/package=BiasCorrector)
[](https://cran.r-project.org/package=BiasCorrector)
[](https://github.com/kapsner/BiasCorrector/actions)
[](https://github.com/kapsner/BiasCorrector/actions)
[](https://github.com/kapsner/BiasCorrector/actions)
[](https://codecov.io/gh/https://github.com/kapsner/BiasCorrector)
[](https://doi.org/10.1002/ijc.33681)
`BiasCorrector` is published in *‘BiasCorrector: fast and accurate
correction of all types of experimental biases in quantitative DNA
methylation data derived by different technologies’ (2021)* in the
*International Journal of Cancer* (DOI:
[https://onlinelibrary.wiley.com/doi/10.1002/ijc.33681](https://doi.org/10.1002/ijc.33681)).
`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: ).
## 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:
``` r
install.packages("BiasCorrector")
```
#### Development version
If you want to use the latest development version, you can install the
github version of `BiasCorrector` with:
``` r
install.packages("remotes")
remotes::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.
``` r
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
``` bash
# 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
``` bash
# 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
.
## 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](https://youtu.be/xOf8uDbUrms).
## Demo Version
A demo version of `BiasCorrector` is available
[here](https://biascorrector.diz.uk-erlangen.de/).
## Frequently Asked Questions
More detailed information on how to use the backend-package
`rBiasCorrection` can be found in its
[vignette](https://cran.r-project.org/web/packages/rBiasCorrection/vignettes/rBiasCorrection_howto.html).
The FAQs can be found
[here](https://github.com/kapsner/rBiasCorrection/blob/master/FAQ.md).
## Citation
L.A. Kapsner, M.G. Zavgorodnij, S.P. Majorova, A. Hotz‐Wagenblatt, O.V.
Kolychev, I.N. Lebedev, J.D. Hoheisel, A. Hartmann, A. Bauer, S. Mate,
H. Prokosch, F. Haller, and E.A. Moskalev, BiasCorrector: fast and
accurate correction of all types of experimental biases in quantitative
DNA methylation data derived by different technologies, Int. J. Cancer.
(2021) ijc.33681.
doi:[10.1002/ijc.33681](https://onlinelibrary.wiley.com/doi/10.1002/ijc.33681).
``` bibtex
@article{kapsner2021,
title = {{{BiasCorrector}}: Fast and Accurate Correction of All Types of Experimental Biases in Quantitative {{DNA}} Methylation Data Derived by Different Technologies},
author = {Kapsner, Lorenz A. and Zavgorodnij, Mikhail G. and Majorova, Svetlana P. and Hotz-Wagenblatt, Agnes and Kolychev, Oleg V. and Lebedev, Igor N. and Hoheisel, J{\"o}rg D. and Hartmann, Arndt and Bauer, Andrea and Mate, Sebastian and Prokosch, Hans-Ulrich and Haller, Florian and Moskalev, Evgeny A.},
year = {2021},
month = may,
pages = {ijc.33681},
issn = {0020-7136, 1097-0215},
doi = {10.1002/ijc.33681},
journal = {International Journal of Cancer},
language = {en}
}
```
## More Infos
- Original work by Moskalev et al.: https://doi.org/10.1093/nar/gkr213
- about Shiny: https://www.rstudio.com/products/shiny/
- RStudio and Shiny are trademarks of RStudio, Inc.
- about Docker: https://www.docker.com/