{"id":19994045,"url":"https://github.com/kapsner/biascorrector","last_synced_at":"2025-05-04T13:30:47.086Z","repository":{"id":37406230,"uuid":"159047781","full_name":"kapsner/BiasCorrector","owner":"kapsner","description":"R package providing a shiny GUI to the functions implemented in 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BiasCorrector\n\n\u003c!-- badges: start --\u003e\n\n[![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![](https://www.r-pkg.org/badges/version/BiasCorrector)](https://cran.r-project.org/package=BiasCorrector)\n[![CRAN\nchecks](https://badges.cranchecks.info/worst/BiasCorrector.svg)](https://cran.r-project.org/web/checks/check_results_BiasCorrector.html)\n[![](http://cranlogs.r-pkg.org/badges/grand-total/BiasCorrector?color=blue)](https://cran.r-project.org/package=BiasCorrector)\n[![](http://cranlogs.r-pkg.org/badges/last-month/BiasCorrector?color=blue)](https://cran.r-project.org/package=BiasCorrector)\n[![Dependencies](https://tinyverse.netlify.app/badge/BiasCorrector)](https://cran.r-project.org/package=BiasCorrector)\n[![R build\nstatus](https://github.com/kapsner/BiasCorrector/workflows/R%20CMD%20Check%20via%20%7Btic%7D/badge.svg)](https://github.com/kapsner/BiasCorrector/actions)\n[![R build\nstatus](https://github.com/kapsner/BiasCorrector/workflows/lint/badge.svg)](https://github.com/kapsner/BiasCorrector/actions)\n[![R build\nstatus](https://github.com/kapsner/BiasCorrector/workflows/test-coverage/badge.svg)](https://github.com/kapsner/BiasCorrector/actions)\n[![](https://codecov.io/gh/https://github.com/kapsner/BiasCorrector/branch/main/graph/badge.svg)](https://codecov.io/gh/https://github.com/kapsner/BiasCorrector)\n[![](https://img.shields.io/badge/doi-10.1002/ijc.33681-yellow.svg)](https://doi.org/10.1002/ijc.33681)\n\n\u003c!-- badges: end --\u003e\n\n`BiasCorrector` is published in *‘BiasCorrector: fast and accurate\ncorrection of all types of experimental biases in quantitative DNA\nmethylation data derived by different technologies’ (2021)* in the\n*International Journal of Cancer* (DOI:\n[https://onlinelibrary.wiley.com/doi/10.1002/ijc.33681](https://doi.org/10.1002/ijc.33681)).\n\n`BiasCorrector` is the user friendly implementation of the algorithms\ndescribed by Moskalev et. al in their research article *‘Correction of\nPCR-bias in quantitative DNA methylation studies by means of cubic\npolynomial regression’*, published 2011 in *Nucleic acids research,\nOxford University Press* (DOI: \u003chttps://doi.org/10.1093/nar/gkr213\u003e).\n\n## Installation\n\n### Using R\n\n- Make sure, you have R installed on your system:\n\n  - https://cran.r-project.org/\n\n- Then open your development environment and install this R package:\n\n#### CRAN version\n\nYou can install `BiasCorrector` simply with via R’s `install.packages`\ninterface:\n\n``` r\ninstall.packages(\"BiasCorrector\")\n```\n\n#### Development version\n\nIf you want to use the latest development version, you can install the\ngithub version of `BiasCorrector` with:\n\n``` r\ninstall.packages(\"remotes\")\nremotes::install_github(\"kapsner/BiasCorrector\")\n```\n\n- To start BiasCorrector, just run the following command in R. A browser\n  tab should open displaying BiasCorrector. Alternatively you can type\n  the URL “localhost:3838/” in your browser.\n\n``` r\nlibrary(BiasCorrector)\nlaunch_app()\n```\n\n### Using Docker\n\nTo simplify installation an deployment of `BiasCorrector` you can clone\nthis repository and build your own docker image. Make sure, you have\nDocker and docker-compose installed on your system.\n\n#### Build Docker Image Manually\n\n``` bash\n# clone the repository\ngit clone https://github.com/kapsner/BiasCorrector\n\n# go to the docker subfolder\ncd BiasCorrector/docker/\n\n# run the build script\n./build_image.sh\n\n# when the building is finished, just start the container by running\ndocker-compose -f docker-compose.local.yml up -d\n```\n\n#### Using a Remote Docker Image\n\n``` bash\n# clone the repository\ngit clone https://github.com/kapsner/BiasCorrector\n\n# go to the docker subfolder\ncd BiasCorrector/docker/\n\n# start the Docker container\ndocker-compose -f docker-compose.remote.yml up -d\n```\n\nType the URL “localhost:3838/” in your browser and start working with\n`BiasCorrector`.\n\n## rBiasCorrection\n\n`BiasCorrector` depends on the `rBiasCorrection` R-package, which is the\nimplementation of the core functionality to correct measurement biases\nin DNA methylation analyses. `BiasCorrector` brings this functionality\nto a user-friendly shiny web application.  \n`rBiasCorrection` is available at\n\u003chttps://github.com/kapsner/rBiasCorrection\u003e.\n\n## Video Tutorial\n\nA video tutorial describing the workflow of how to use `BiasCorrector`\nin order to correct measurement bias in DNA methylation data is\navailable [on youtube](https://youtu.be/xOf8uDbUrms).\n\n## Demo Version\n\nA demo version of `BiasCorrector` is available\n[here](https://biascorrector.diz.uk-erlangen.de/).\n\n## Frequently Asked Questions\n\nMore detailed information on how to use the backend-package\n`rBiasCorrection` can be found in its\n[vignette](https://cran.r-project.org/web/packages/rBiasCorrection/vignettes/rBiasCorrection_howto.html).\nThe FAQs can be found\n[here](https://github.com/kapsner/rBiasCorrection/blob/master/FAQ.md).\n\n## Citation\n\nL.A. Kapsner, M.G. Zavgorodnij, S.P. Majorova, A. Hotz‐Wagenblatt, O.V.\nKolychev, I.N. Lebedev, J.D. Hoheisel, A. Hartmann, A. Bauer, S. Mate,\nH. Prokosch, F. Haller, and E.A. Moskalev, BiasCorrector: fast and\naccurate correction of all types of experimental biases in quantitative\nDNA methylation data derived by different technologies, Int. J. Cancer.\n(2021) ijc.33681.\ndoi:[10.1002/ijc.33681](https://onlinelibrary.wiley.com/doi/10.1002/ijc.33681).\n\n``` bibtex\n@article{kapsner2021,\n  title = {{{BiasCorrector}}: Fast and Accurate Correction of All Types of Experimental Biases in Quantitative {{DNA}} Methylation Data Derived by Different Technologies},\n  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.},\n  year = {2021},\n  month = may,\n  pages = {ijc.33681},\n  issn = {0020-7136, 1097-0215},\n  doi = {10.1002/ijc.33681},\n  journal = {International Journal of Cancer},\n  language = {en}\n}\n```\n\n## More Infos\n\n- Original work by Moskalev et al.: https://doi.org/10.1093/nar/gkr213\n- about Shiny: https://www.rstudio.com/products/shiny/\n- RStudio and Shiny are trademarks of RStudio, Inc.\n- about Docker: https://www.docker.com/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkapsner%2Fbiascorrector","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkapsner%2Fbiascorrector","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkapsner%2Fbiascorrector/lists"}