Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
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Oct 31, 2025 - Nextflow
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proteogenomics
Here are 35 public repositories matching this topic...
PDV: an integrative proteomics data viewer
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Jul 12, 2025 - Java
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
workflow pipeline nextflow proteomics dia mass-spectrometry openms proteogenomics tmt nf-core mass-spec lfq
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May 6, 2024 - Nextflow
Multi-Omics Peptide Generator
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Oct 31, 2025 - Python
NeoFlow: a proteogenomics pipeline for neoantigen discovery
proteogenomics nextflow-pipeline neoantigen-prediction novel-peptide-identifications neoantigen-discovery
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Nov 16, 2024 - Nextflow
Library for mass spectrometry projects
chemistry mass-spectrometry chemical-formulas isotopes proteomics-data spectra-files proteogenomics mass-spectrometry-data
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Oct 24, 2025 - C#
Python tools for proteogenomics analysis toolkit
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Apr 26, 2024 - Python
PepQuery: a targeted peptide search engine
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May 1, 2024 - Java
Proteogenomics database-generation tool for protein haplotypes and variants
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Jun 19, 2025 - Python
Customized protein database construction
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Jul 12, 2025 - Java
PGA: a tool for ProteoGenomics Analysis
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Mar 8, 2022 - R
This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.
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Sep 25, 2024 - JavaScript
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
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Jun 19, 2024 - C#
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
workflow pipeline nextflow proteomics cosmic proteogenomics nf-core protein-databases gnomad pypgatk
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Jan 13, 2025 - Nextflow
PGATK: ProteoGenomics Analysis ToolKit
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Aug 19, 2021
Research into statistical distributions of genomes, proteomes and reactomes
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Feb 14, 2022 - Scheme
A python library with scripts and helpers classes for quantms workflow
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May 14, 2025 - Python
Saccharomyces cerevisiae information, gene calling and ORF identification assistant
machine-learning ai genomics chatbot-application model-organisms gradio sequence-classification proteogenomics research-assistant saccharomyces-cerevisiae pilot-project generative-ai gene-calling
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Apr 15, 2024 - Python
6-frame proteogenomic peptide-spectrum match identification engine
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Sep 4, 2022 - Java
PepQueryMHC: Rapid and Comprehensive Tumor Antigen Prioritization from Immunopeptidomics Data
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Oct 8, 2025 - Java
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