DIAgui is an R package that contains a user-friendly shiny app to process output from DIA-nn proteomics software. Since shiny can be quite slow to process big data file, a function that does the complete workflow and saves all results in a directory is also present. The process is as follow: filtering data according q.values, applying MaxLFQ algorithm for quantification, getting some other informations, plot some graphs to check data quality.
This package is based on diann-rpackage from Vadim Demichev. The c++ source code is exactly the same as the one from V.Demichev, it is used for MaxLFQ algorithm. You can also use iq R package which is way faster to run MaxLFQ algorithm.
In addition to filter data and calculate MaxLFQ intensities, you can also get the Top3 and iBAQ quantification within the app.
DOI: https://doi.org/10.1093/bioadv/vbae001
- R version >= 4.0
- Rstudio
Go to Rstudio. Install DIAgui from github:
if(!requireNamespace("devtools", quietly = TRUE)){
install.packages("devtools")
}
devtools::install_github("marseille-proteomique/DIAgui")You can now load it and run the app with this commands:
library(DIAgui)
runDIAgui()If you want to learn more about the app, check the tutorial !
If you want to test the application, you can download a toy dataset here which contain a small report from saccharomyces cerevisiae with its corresponding FASTA file. For information about the data, you access access its documentation in R via ?small_report