Reverse Dependencies of pyteomics

The following projects have a declared dependency on pyteomics:

• AA-stat — A utility for validation of peptide identification results in proteomics using amino acid counting.
• aiproteomics — A package for MSMS spectral library prediction models from the field of (phospho-)proteomics, intended to facilitate the testing and comparison of different neural network architectures and existing models.
• alphabase — An infrastructure Python package of the AlphaX ecosystem
• alphamap — Peptide level analysis of bottom-up proteomics data
• alphastats — An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics
• alphaviz — A interactive Dashboard to explore mass spectrometry data.
• Biosaur — Proteomics post-search algorithm
• biosaur2 — A feature detection LC-MS1 spectra.
• breathXplorer — A toolkit for breath metabolomics analysis
• casanovo — De novo mass spectrometry peptide sequencing with a transformer model
• casanovogui — A streamlit GUI for the casanovo.
• cascadia — De novo sequencing for DIA mass spectrometry data
• crema-ms — Confidence estimation for proteomics experiments
• DecoID — Metabolomics software for database assisted deconvolution of MS/MS spectra
• depthcharge-ms — A mass spectrometry toolkit for deep learning with Transformer models.
• diffacto — A protein summarization method for shotgun proteomics experiments
• dleamse — dleamse's encoding and embedding methods, and dleamse's faiss index (IndexIDMap type) write.
• elfragmentador — Predicts peptide fragmentations using transformers
• falcon-ms — Large-scale tandem mass spectrum clustering using fast nearest neighbor searching
• fastg2protlib — FASTG sequences to a protein library
• fermo_core — Data processing/analysis functionality of metabolomics dashboard FERMO
• fragannot — A python CLI app for fragment annotation
• glycresoft — Glycan and Glycopeptide Mass Spectrometry Database Search Tool
• ibench — Benchmarking for mass spectrometry identifications.
• inspirems — Helping to integrate Spectral Predictors and Rescoring.
• Ion-networks — Analysis of LC-[...]-MSMS data with ion-networks
• IPTKL — IPTK is a library specialized in the analysis of HLA-peptidomes identified through an immunopeptidomics pipeline.
• iqmma — A MS1 feature mapping for MS2 spectra identifications.
• lslcharge — A deep learning toolkit for proteomics, equipped with a few tools for network recycling.
• masscube — Accurate and fast data processing for metabolomics
• massql — Mass spectrometry query language python implementation
• matchms — Python library for large-scale comparisons and processing of tandem mass spectral data
• mmproteo — Mirko meets Proteomics: A PRIDE Archive downloader and file converter
• molnetpack — 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
• morley — GUI software for plant morphometry
• ms-deisotope — Access, Deisotope, and Charge Deconvolute Mass Spectra
• ms-entropy — This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data.
• ms-mint — Metabolomics Integrator (Mint)
• ms1searchpy — A proteomics search engine for LC-MS1 spectra.
• ms2ml — Provides an intermediate layer between mass spec data and ML applications, such as encoding.
• ms2rescore — MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.
• msdataviewer — A package for handling SQT format ProLucid search files
• mskit — Utils for MS data processing
• mzspeclib — HUPO-PSI Spectral library format
• patpat — Patpat is public proteomics dataset search framework that only requires protein identifiers to be passed in to search for relevant datasets.
• peptdeep — The AlphaX deep learning framework for Proteomics
• pmultiqc — Python package for quality control of proteomics datasets, based on multiqc package
• PoolSeqProGen — A package for creating variant protein databases for bacteria from Pool-seq experiments
• PowerNovo — PowerNovo: A New Efficient Tool for De Novo Peptide Sequencing
• protein-turnover — protein turnover pipeline
• ProteoformQuant — A python command line tool for the quantification of peptidoform/proteoforms
• proteomics-downstream-analysis — A package for downstream data analysis of proteomics data
• psm-utils — Common utilities for parsing and handling peptide-spectrum matches and search engine results.
• pyascore — A python module for fast post translational modification localization.
• pyhxexpress — pyHXExpress
• pypgatk — Python tools for proteogenomics
• pyproteininference — Python Package for running custom protein inference algorithms on tab-formatted tandem MS/MS search results.
• pyteomics.cythonize — An Cython-accelerated version of common pyteomics functions
• pyteomics.pepxmltk — A utility for creation of pepXML files from Python objects and TandemXML files.
• sagepy — no summary
• SAMPEI — SAMPEI
• Scavager — Proteomics post-search algorithm
• searchcake — tpp search workflow with peptideprophet and proteinprophet staring from mzXML files
• seq-to-first-iso — Compute first two isotopologues intensity from peptide sequence.
• simsalabim — Simple Interface for MS Applications
• spectrum-io — IO related functionalities for oktoberfest.
• spectrum-utils — Mass spectrometry utility functions
• synthedia — Generate synthetic DIA LC-MS/MS proteomics data
• xi-mzidentml-converter — xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a relational database (PostgreSQL or SQLite) using sqlalchemy.
• xiRT — xiRT: Multi-dimensional Retention Time Prediction for Linear and Crosslinked Peptides.
• xiutilities — A collection of corss-link mass spectrometry tools.
• zoDIAq — Bioinformatics software package for identifying peptides and proteins in DIA and DISPA mass spectrometry data files.