ypriverol

quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

cluster-analysis

A set of R scripts to analyse the data from PRIDE Cluster

CompProt2019-paper

This repository store the content of a Computational Proteomics manuscript Trends and Opportunities by 2019

containers-rules-manuscript

Recommendations to contenarized your bioinformatics software

customprodbj

github-paper

Plos in Computational Biology paper related with github for researchers, code, source and document

os-proteomics

View point in Open source in Proteomics

proteomics-metadata-standard

The Proteomics Experimental Design file format: Standard for experimental design annotation

spark-java8

Java 8 and Spark learning through examples

visualisation-manuscript-examples

ypriverol/os-proteomics

View point in Open source in Proteomics

ypriverol/CompProt2019-paper

This repository store the content of a Computational Proteomics manuscript Trends and Opportunities by 2019

ypriverol/quantms-research

This repository contains a set of JupyterNotebooks and code with analysis and plots for the pipeline https://github.com/bigbio/quantms

ypriverol/proteomics-metadata-standard

The Proteomics Experimental Design file format: Standard for experimental design annotation

ypriverol/annotator

SDRF for proteomics annotator

ypriverol/bioconda-recipes

Conda recipes for the bioconda channel.

ypriverol/biosaur2

ypriverol/chat-langchain

ypriverol/containers-fork

Bioinformatics containers

ypriverol/FDRBench

Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment

ypriverol/mimic

A decoy database scrambler that conserves homology

ypriverol/MSnet

A large open benchmark dataset for computational proteomics

ypriverol/mzIdentML

Repository for mzIdentML and the corresponding examples

ypriverol/ontollm

A simple tool fo search free-text on OBO ontologies using LLMs (research tool)

ypriverol/OpenMS

The codebase of the OpenMS project

ypriverol/presentations

ypriverol/pride-molecule-indexer

NextFlow and NF-Core workflow that convert PRIDE Complete submissions to json files including PSMs, Peptides and Proteins.

ypriverol/ProteoWorks

Workshops for Proteomics Data Analysis Tasks by Bioinformaticians at Lehtio Lab

ypriverol/psi-ms-CV

HUPO-PSI mass spectrometry CV

ypriverol/psi-tools

Previous https://sourceforge.net/p/psidev/svn/HEAD/tree/psi/tools/ folder

ypriverol/python-scripts

ypriverol/quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

ypriverol/sdrf-pipelines

Different python tools to validate and convert SDRF files

ypriverol/sdrfcheck-api

A flask API for the SDRF annotator tool

ypriverol/staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

ypriverol/tdf2mzml

ypriverol/ThermoRawFileParser

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

ypriverol/timsconvert

ypriverol/xlmod-CV

Repo for the XLMOD ontology for chemical cross linkers

ypriverol/ypriverol