RaMS - R Access to Mass-Spec Data
R-based access to mass-spectrometry (MS) data. While many packages exist to process MS data, many of these make it difficult to access the underlying mass-to-charge ratio (m/z), intensity, and retention time of the files themselves. This package is designed to format MS data in a tidy fashion and allows the user perform the plotting and analysis.
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mass-spectrometry-datatidy-data
8.60 score 25 stars 8 dependents 132 scripts 723 downloadsggtintshade - Tinting and Shading Aesthetics for 'ggplot2'
Adds a tintshade aesthetic to 'ggplot2' that varies the lightness of a mapped colour or fill within each hue group, keeping the plotted layer and its legend in sync. Supports both nested designs (each item belongs to one hue) and crossed designs (each lightness level appears across hues).
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5.38 score 8 stars 6 scripts 188 downloadssquallms - Speedy quality assurance via lasso labeling for LC-MS data
squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.
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massspectrometrymetabolomicsproteomicslipidomicsshinyappsclassificationclusteringfeatureextractionprincipalcomponentregressionpreprocessingqualitycontrolvisualization
4.48 score 3 stars 7 scripts 226 downloads