An AnnData-based framework for integrated proteomics analysis
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Aug 30, 2026 - Python
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proteoforms
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A Nextflow pipeline for end-to-end long-read proteogenomics analysis
rna-seq alternative-splicing proteomics mass-spectrometry splicing-quantification isoforms proteogenomics splicing-analyses long-read-sequencing protein-analysis splicing nextflow-pipeline proteoforms isoform-diversity rna-analysis rna-isoforms
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Aug 29, 2026 - Nextflow
Mirage generates multiple sequence alignments of proteoforms by mapping sequences back to their coding regions on the genome and then compressing those mappings into alignments.
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Jun 27, 2025 - Perl
PathwayMatcher is a free, open-source software to search for pathways related to a list of proteins in Reactome. This repository is the development repository. For the latest version see: https://github.com/PathwayAnalysisPlatform/PathwayMatcher
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Mar 4, 2019 - Java
HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data
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Oct 16, 2022 - Python
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