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It is aimed at alleviating reproducibility issues and pernicious effects of deviating signals on both data pre-processing and downstream data analysis. Based on robust statistical methods, it facilitates the identification and filtering of low-quality mass spectra and atypical peak profiles as well as monitoring and data handling through pre-processing, which extends existing computational tools for MS data. `MALDIrppa` integrates with and extends existing R packages for MS proteomics data. Helper functions are included that allow to export data into formats used for downstream analyses.\n\n### Installation\n\nThe latest version of the package is available on CRAN and can be installed from R using\n\n```\ninstall.packages(\"MALDIrppa\")\n```\n\nAlternatively, it can be installed from Github through the `devtools` package:\n\n```\n# For non-windows users\ndevtools::install_github(repo = \"Japal/MALDIrppa\")\n# For windows users\ndevtools::install_url(url=\"https://github.com/Japal/MALDIrppa/archive/master.zip\", INSTALL_opt= \"--no-multiarch\")\n```\n\nFor compatibility with previous pre-processing pipelines, a previous version of MALDIrppa can be installed from source files. For example, for v1.0.5-1:\n\n```\ninstall.packages(\"https://cran.r-project.org/src/contrib/Archive/MALDIrppa/MALDIrppa_1.0.5-1.tar.gz\", repo=NULL, type=\"source\")\n```\n\n\n### Getting started\n\n```\n# Loading the library\nlibrary(\"MALDIrppa\")\n```\n\nDocumentation and examples are available through the help pages (`?MALDIrppa`).\n\n### Illustrative pipeline\n\nThe package's vignette provides a walk through the main features and functions:\n\n* Article on website: https://japal.github.io/MALDIrppa/\n* CRAN: https://cran.r-project.org/web/packages/MALDIrppa/vignettes/MALDIrppa_vignette.html\n\n### Citation\n\nPalarea-Albaladejo J., McLean K., Wright F. and Smith (2018). MALDIrppa: quality control and robust analysis for mass spectrometry data. Bioinformatics 34(3):522–523. \u003cdoi: http://dx.doi.org/10.1093/bioinformatics/btx628\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjapal%2Fmaldirppa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjapal%2Fmaldirppa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjapal%2Fmaldirppa/lists"}