Yasset Perez-Riverol

Filters for PSM-Peptides using Search Engine provisioning

3

Some pipelines need to filter PSMs taking into account the Search Engine provisioning (which search engines have identified the corresponding spectrum), we see two cased here: - [x] Filter Peptides...

We should implement a way to provide parameters in Json or yaml file and move out of xml confía file.

We need to have a way of computing the FDR for classes of PSMs - Peptides and Proteins. This classes can be : - [ ] General Modified: FDR for...

Parsing the PepXML files

1

We need to be able to parse the pepXML files which enable to support original results from TPP and other search engines.

The PIAModeller which contains all the nice functions should consume a file (or PIACompiler) instead of PIA compilation file

1

Currently, the only way to apply some statistics on top of a standard file format is with PIACompiler and this needs to be written in an PIA file to be...

DIANN error big dataset

5

Hi @vdemichev I'm trying to run a large experiment with quantms. In the latest step of quantms, I got the following error: ``` pst_prd@codon-dm-05:/hps/nobackup/juan/pride/reanalysis/absolute-expression/platelet/PXD039236$ tail -n 500 -f work/40/916f1229262d23cf0064ad40e0ef38/assemble_empirical_library.log DIA-NN...

PhosphoRS score without Annotations

1

Hi @mvaudel do you think would be possible to implement phosphoRS without the fragment annotations. That means if I give you a peptide sequence, spectrum, modification, and positions. ?

Parquet needs some standarization

2

We need to do some standardization for the Parquet format that enables other people to understand the file format.

self contain app

5

@caetera @nielshulstaert can we explore how to release self contain an application for the converter

Opening a database from exiting data does not work

5

Hi: I'm using levelDB for one of my projects and I found that when I copy one of my directories of levelDB and try to read it again it doesn't...