Data

Tools

Indexes

Applications

Experiments

Open Source Science

biascorrector

R package providing a shiny GUI to the functions implemented in rBiasCorrection

https://github.com/kapsner/biascorrector

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 13 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bias-correction cran gene-methylation genetics gui pcr r r-package shiny
Last synced: 6 months ago · JSON representation

Repository

R package providing a shiny GUI to the functions implemented in rBiasCorrection

Basic Info
  • Host: GitHub
  • Owner: kapsner
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 526 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
bias-correction cran gene-methylation genetics gui pcr r r-package shiny
Created about 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

BiasCorrector

CRAN checks Dependencies R build status R build status R build status

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).

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:

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 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

More detailed information on how to use the backend-package rBiasCorrection can be found in its vignette. The FAQs can be found here.

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.

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/

Owner

  • Login: kapsner
  • Kind: user
  • Location: Erlangen, Germany

Medical Data Scientist.

GitHub Events

Total
  • Push event: 4
  • Create event: 2
Last Year
  • Push event: 4
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 271
  • Total Committers: 2
  • Avg Commits per committer: 135.5
  • Development Distribution Score (DDS): 0.004
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kapsner l****r@w****e 270
Kapsner k****z@m****e 1
Committer Domains (Top 20 + Academic)
medads.uk-erlangen.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • kapsner (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 393 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
  • Total maintainers: 1
cran.r-project.org: BiasCorrector

A GUI to Correct Measurement Bias in DNA Methylation Analyses

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 393 Last month
  • Docker Downloads: 21,613
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Average: 32.0%
Downloads: 34.4%
Dependent repos count: 35.5%
Maintainers (1)
lorenz.kapsner@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • DT * imports
  • data.table * imports
  • magrittr * imports
  • rBiasCorrection >= 0.3.4 imports
  • shiny * imports
  • shinydashboard * imports
  • shinyjs * imports
  • lintr * suggests
  • testthat * suggests
.github/workflows/coverage.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • pat-s/always-upload-cache main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
.github/workflows/lint.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • pat-s/always-upload-cache main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
.github/workflows/tic.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • actions/upload-artifact main composite
  • pat-s/always-upload-cache main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
docker/Dockerfile docker
  • rocker/shiny-verse 4.0.4 build
docker/docker-compose.local.yml docker
  • biascorrector latest
docker/docker-compose.remote.dev.yml docker
  • harbor.miracum.org/biascorrector/biascorrector_img latest
docker/docker-compose.remote.yml docker
  • harbor.miracum.org/biascorrector/biascorrector_img 0.1.4