Ethan Bass

chromatographR : Chromatographic Data Analysis Toolset Github



chromatographR provides a set of tools for flexibly and reproducibly analyzing HPLC-DAD data or other "simple" chromatographic data (e.g. HPLC-UV, GC-FID) in R. Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. For an example workflow, see the vignette.

chromConverter : Chromatographic File Converter Github



chromConverter reads chromatograms from a variety of proprietary formats into R objects. It currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw' files as well as various text-based formats. In addition to its internal file parsers, chromConverter provides a simple programmatic interface to file parsers from several external libraries, such as Aston, Entab, OpenChrom, rainbow, and the ThermoRawFileParser.

mzinspectr: Read and Analyze Mass Spectrometry Alignment Files . Github

There are many wonderful open source tools for analyzing mass spectrometry data like MS-DIAL and MZmine, however these tools are not as flexible as R for downstream statistical analyses of the resulting feature tables. Rather than re-inventing the wheel, I wanted a tool that could be used to flexibly analyze MS alignments in R. The mzinspectr package makes it easy to import feature tables from other programs for further processing and analysis in R. It includes functions for normalization, feature identification, and visualization of mass spectra.

ggtukey: Compact Letter Displays for 'ggplot2' . Github

The ggtukey package provides a simple way to visualize paired comparisons by adding compact letter displays to 'ggplot2' figures. The example shows differences in body mass between penguin species, using data from the palmerpenguins package. To get started, visit the vignette.

zerenebatchR: Utility for Batch Processing Images in Zerene Stacker . Github

zerenebatchR is a utility I made in R to facilitate easier stacking of photos with Zerene Stacker . I use it mainly for stacking pictures of mycorrhizal hyphae (as pictured on the right) and root structures to measure the performance of mycorrhizae.

ShinyChromViewer: Shiny Gadget for Interactive Viewing and Exploration of Chromatograms . Github

A Shiny app for interactively viewing HPLC-DAD chromatograms in R.

r2zotero: Send Suggested R Package Citations Directly to Zotero . Github

A utility to facilitate the citation of R packages by importing citations from 'CITATION' file directly to a local Zotero library using the Zotero Web API.