{"repo":"nf-core/diaproteomics","free":true,"listed":false,"github":"https://github.com/nf-core/diaproteomics","clone":"git clone https://github.com/nf-core/diaproteomics.git","description":"Automated quantitative analysis of DIA proteomics mass spectrometry measurements.","language":"Nextflow","stars":21,"topics":["nf-core","nextflow","workflow","pipeline","proteomics","data-independent-proteomics","dia-proteomics","openms"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Automated quantitative analysis of DIA proteomics mass spectrometry measurements. Introduction nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data (preprint available here). The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. Optionally, spectral libraries can be generated (EasyPQP) from multiple matched DDA measurments and respective search results. Generated libraries can then further be aligned applying a pairwise RT alignment and concatenated into a single large library. In the same way internal retention time standarts (irts) can be either supplied or generted by the workflow in order to align library and DIA measurements into the same retention time space. FDR rescoring is applied using Pyprophet based on a competitive target-decoy approach on peakgroup or global peptide and protein level. In a last step DIAlignR for chromatogram alignment and quantification is carried out and a csv of peptide quantities, MSstats based protein statistics and several visualisations are exported. (This chart was created with the help of Lucidchart) Quick Start 1. Install nextflow 2. Install any of Docker , Singularity , Podman , Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs) 3. Download the pipeline and test it on a","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/diaproteomics/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}