Marco Chiapello

Hi Julian, thank you for the quick reply. I just started working with DIA and I have not real experience with OpenSwath, but I believe it can not work with...

> PIA should work with DIA data as well, as long as you only want to look at the identification values This means PIA is not doing any quantification, right?

> Right, PIA can only create the protein grouping on the given peptide identifications. This information can be passed on to protein quantifiers, though. It works currently nice together with...

I enquired the openswath's developer, here the replay: > As input, OpenSWATH requires spectral libraries and it supports HUPO-PSI > TraML, which can be generated from pepXML/mzIdentML/idXML via SpectraST. Is...

Thank you! I will try asap and I let you know

The plan is: 1. Use PIA on DDA searches 1. Format the result file into TraML 1. Use OpenSwath to do the DIA analysis Do you think we need one...

Currently, ggplot2 offers a range of shapes, but drawing wavy lines isn't directly supported. This feature would be valuable for various visualizations (trends, design elements, scientific diagrams). I've seen others...

Here an example: 

I run the following pipeline: ``` pyprophet score --in data/osw_output.osw --protein pyprophet protein --in data/osw_output.osw --context run-specific pyprophet export --in data/osw_output.osw --out data/protein_inference_FDR001.tsv --protein feature_alignment.py --in data/protein_inference_FDR001.tsv --out data/TRIC_protein_inference_FDR001.tsv --method...

Here the bit of quarto code ``` --- title: "Introduzione all' RNASeq" author: "Marco Chiapello, PhD" date: "01/04/2023" institute: "Tor Vergata" format: revealjs: #incremental: true logo: images/cropped-cropped-logo-1-10.png #footer: "`emitanaka.org/slides/toronto2022`" slide-number:...