msTrawler

A toolkit for analyzing multiplexed proteomics data with an emphasis on finding a reliability threshold and accounting for signal dependent heteroskedactity.

Installation

Option 1: Using devtools

devtools::install_github("https://github.com/calico/msTrawler")

Option 2: from source

1. clone or pull repo

git clone [email protected]:calico/msTrawler.git

2. cd to parent directory

cd ~/workspace

3. install with --no-staged-install flag

R CMD INSTALL msTrawler --no-staged-install

the --no-staged-install option is essential, otherwise will not build.

4. test in RStudio

library(msTrawler)

4. test converting proteome discoverer ouput to R dataframe 

setwd("/PATH/TO/LIBRARY/FOLDER") df <- convertPdFile("data/pd_example_export_PSMs.txt", "data/pd_example_export_Proteins.txt")

5.  For help using the package please see the tutorial here
...
https://github.com/calico/msTrawler/blob/main/msTrawler_tutorial.pdf
...