Data filtering

[pejota66]

Hello

Does the Fragpipe-analyst performs the data filtering (i.e. removing proteins classified as Only identified by site,
Contaminants, and Reverse)?

Is it possible to retrieve the R-script of the analyst and use it in R

Thank you

[hsiaoyi0504]

@pejota66 The R code of FragPipe-Analyst is here: https://github.com/MonashProteomics/FragPipe-Analyst.
For the data filtering part, contaminants and reverse peptides are removed but not necessary in FragPipe-Analyst. The majority of them were removed when you ran the FragPipe.