README.md

In chasemc/GNPSeasy:

GNPSeasy

Fair Warning: Author has no affiliation with the GNPS team

This is a low-priority weekend project so it's currently a Work In Progress.

The initial idea is for this to be as a low-level, easy-to-use R Shiny App for people to convert raw mass spectrometry data to the proper .mzXML format for use with GNPS. Also included are plots (with easy download) for rapidly diagnosing problems there might be with the data.

Once most of the kinks are worked out I will compile it into an exe for simple installation and use so users unfamiliar with R can use it.

For now... to use:

One folder up from app.R should live the folder "packageLibrary" under which msconvert lives in the following directory structure:

• "packageLibrary"
• "proteowizardinstallation"
  • "pwiz"
  • "msconvert.exe"

In the same folder as msconvert.exe are all the dlls, etc (can just copy/paste the entire proteowizard installation.

R v3.5.0 Packages Needed:

install.packages("shiny")
install.packages("devtools")
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")
source("https://bioconductor.org/biocLite.R")
biocLite("MSnbase")
devtools::install_github("thomasp85/patchwork")
devtools::install_github("tidyverse/ggplot2@4463da6")
install.packages("ggplot2")
install.packages("gridExtra")
install.packages("svglite")

Current Bugs:

To see the plots of converted data you will need to wait for the conversions to finish... unless you already have mzXML files, in which case you can directly select the folder that contains those mzXML files by clicking the "Click to select where mzXML files should be created" button.

chasemc/GNPSeasy documentation built on May 30, 2019, 4:02 p.m.