Yasset Perez-Riverol's repositories
quantms-research
This repository contains a set of JupyterNotebooks and code with analysis and plots for the pipeline https://github.com/bigbio/quantms
proteomics-metadata-standard
The Proteomics Experimental Design file format: Standard for experimental design annotation
bioconda-recipes
Conda recipes for the bioconda channel.
containers-fork
Bioinformatics containers
DiaNN
DIA-NN - a universal automated software suite for DIA proteomics data analysis.
ibaqpy
Trying out some ibaq code with pyopenms
mimic
A decoy database scrambler that conserves homology
MSnet
A large open benchmark dataset for computational proteomics
mzIdentML
Repository for mzIdentML and the corresponding examples
OpenMS
The codebase of the OpenMS project
pride-archive-api
PRIDE Archive public Restful API
pride-molecule-indexer
NextFlow and NF-Core workflow that convert PRIDE Complete submissions to json files including PSMs, Peptides and Proteins.
ProteoWorks
Workshops for Proteomics Data Analysis Tasks by Bioinformaticians at Lehtio Lab
psi-ms-CV
HUPO-PSI mass spectrometry CV
psi-tools
Previous https://sourceforge.net/p/psidev/svn/HEAD/tree/psi/tools/ folder
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
sdrf-pipelines
Different python tools to validate and convert SDRF files
sdrfcheck-api
A flask API for the SDRF annotator tool
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
test-datasets
Test data to be used for automated testing with the nf-core pipelines
ThermoRawFileParser
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
xlmod-CV
Repo for the XLMOD ontology for chemical cross linkers