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A Rshiny app with multiple tools to work with compounds masses

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arnaudmeng/mstool_rshiny

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mstool_rshiny

This tool has been developped & designed to offer support with chemisty and mass spectrometry calculation and visualization purposes. It encompasses a variety of functions that should enhance the QoL of mass experts and/or chemist by offering a intuitive and efficient graphic interface dedicated to chemistry and mass spectrometry.

Caution

This project is still under developpment.

Help vignettes for application sections

page 1 - load atom mass table

page 2 - define modifier

page 3 - compute compound mass

page 4 - compute adduct mass list

page 5 - predict formula from mass

page 6 - generate compond pools from mass

page 7 - build analytic chemical sequence for mass spectrometry

page 8 - MGF spectrum vizualizer

Prerequisited packages

  • shiny
  • shinydashboard
  • shinyBS
  • shinyalert
  • shinyjs
  • markdown
  • DT
  • tidyverse
  • dplyr
  • stringr
  • stringi
  • httr
  • ggplot2
  • ggpmisc
  • plotly
  • ggpubr
  • magrittr
  • ptable

How to

Simply open the "app.R" in Rstudio then click "Run App"

Or

In command line, do:

runApp("app.R")`

Contributors

All functions and utilities embedded resulted from the collaboration of mass spectrometry expert (Kathleen Rousseau, PhD), chemist expert (Lise Boulard, PhD) and bioinformatic expert (Arnaud Meng, PhD). Metabolomic Core Facility of Pasteur Institute (Paris).

Contact

Arnaud Meng, PhD, Institut Pasteur, Paris, FR

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A Rshiny app with multiple tools to work with compounds masses

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