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The Top 23 Proteomics Open Source Projects

Open source projects categorized as Proteomics
Categories > Proteomics
Containers ⭐ 621
Bioinformatics containers
most recent commit 3 months ago
Openms ⭐ 438
The codebase of the OpenMS project
dependent packages 22total releases 18most recent commit 3 months agopypi pyopenms} Downloads
Training Material ⭐ 284
A collection of Galaxy-related training material
most recent commit 3 months ago
Pypdb ⭐ 258
A Python API for the RCSB Protein Data Bank (PDB)
dependent packages 5total releases 18most recent commit 9 months agopypi pypdb} Downloads
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Lightdock ⭐ 234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
most recent commit 3 months ago
Ckg ⭐ 184
Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph
most recent commit 2 years ago
Sage ⭐ 173
Proteomics search & quantification so fast that it feels like magic
most recent commit 3 months ago
Teachingmaterial ⭐ 161
Various teaching material
most recent commit 3 years ago
Diann ⭐ 152
DIA-NN - a universal automated software suite for DIA proteomics data analysis.
most recent commit 10 months ago
Fragpipe ⭐ 149
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
most recent commit 3 months ago
Alphapept ⭐ 136
A modular, python-based framework for mass spectrometry. Powered by nbdev.
total releases 17most recent commit 5 months ago
Msnbase ⭐ 115
Base Classes and Functions for Mass Spectrometry and Proteomics
most recent commit 4 months ago
Percolator ⭐ 112
Semi-supervised learning for peptide identification from shotgun proteomics datasets
most recent commit 5 months ago
Galaxytools ⭐ 111
🔬📚 Galaxy Tool wrappers
most recent commit 3 months ago
Philosopher ⭐ 104
A complete toolkit for shotgun proteomics data analysis
most recent commit 3 months ago
Famsa ⭐ 101
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
most recent commit 2 years ago
Plass ⭐ 99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
most recent commit a year ago
Pyteomics ⭐ 93
Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
dependent packages 60total releases 71most recent commit 3 months agopypi pyteomics} Downloads
Msfragger ⭐ 83
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
most recent commit 4 months ago
Alphapeptdeep ⭐ 81
Deep learning framework for proteomics
dependent packages 1total releases 25most recent commit 3 months agopypi peptdeep} Downloads
Metamorpheus ⭐ 81
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
total releases 5most recent commit 3 months ago
Rforproteomics ⭐ 69
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
most recent commit a year ago
The 10 Most Depended On Proteomics Open Source Projects
Openms ⭐ 438
The codebase of the OpenMS project
dependent packages 22total releases 18latest release October 13, 2023most recent commit 3 months agopypi pyopenms} Downloads
Mspire ⭐ 11
mass spectrometry proteomics in ruby
dependent packages 7total releases 70latest release May 28, 2014most recent commit 10 years agorubygems mspire} Downloads
Pypdb ⭐ 258
A Python API for the RCSB Protein Data Bank (PDB)
dependent packages 5total releases 18latest release July 24, 2023most recent commit 9 months agopypi pypdb} Downloads
Mokapot ⭐ 31
Fast and flexible semi-supervised learning for peptide detection in Python
dependent packages 5total releases 26latest release September 11, 2023most recent commit 6 months agopypi mokapot} Downloads
Atlas Heatmap ⭐ 6
Heatmap visualizing Expression Atlas data
dependent packages 4total releases 153latest release September 25, 2019most recent commit 2 years agonpm expression-atlas-heatmap-highcharts} Downloads
Exon ⭐ 20
Exon is an OLAP query engine specifically for biology and life science applications.
dependent packages 4total releases 12latest release November 20, 2023most recent commit 3 months agocargo exon-common} Downloads
Pyprophet ⭐ 25
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
dependent packages 2total releases 73latest release December 15, 2022most recent commit 6 months agopypi pyprophet} Downloads
Pythomics ⭐ 16
A library to assist with a variety of -omic analyses. Included are tools for proteomics, transcriptomics, and genomics.
dependent packages 2total releases 44latest release August 03, 2023most recent commit 9 months agopypi pythomics} Downloads
Astir ⭐ 42
astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
dependent packages 2total releases 6latest release June 18, 2021most recent commit 5 months agopypi astir} Downloads
The 10 Latest Releases In Proteomics Open Source Projects
Rustyms ⭐ 7
A rust library for parsing Pro Forma peptides and matching them against MS spectra
dependent packages 1total releases 11latest release December 01, 2023most recent commit 3 months agocargo rustyms} Downloads
Exon ⭐ 20
Exon is an OLAP query engine specifically for biology and life science applications.
dependent packages 4total releases 12latest release November 20, 2023most recent commit 3 months agocargo exon-common} Downloads
Deeplc ⭐ 44
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
dependent packages 1total releases 84latest release November 20, 2023most recent commit 3 months agopypi deeplc} Downloads
Alphapept ⭐ 136
A modular, python-based framework for mass spectrometry. Powered by nbdev.
total releases 17latest release November 15, 2023most recent commit 5 months ago
Ms2rescore ⭐ 32
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
total releases 18latest release November 01, 2023most recent commit 3 months ago
Openms ⭐ 438
The codebase of the OpenMS project
dependent packages 22total releases 18latest release October 13, 2023most recent commit 3 months agopypi pyopenms} Downloads
Mzrecal ⭐ 6
Recalibrate Mass Spectrometry data in mzML format
total releases 9latest release October 10, 2023most recent commit 6 months ago
Sdrf Pipelines ⭐ 12
A repository to convert SDRF proteomics files into pipelines config files
dependent packages 1total releases 22latest release September 17, 2023most recent commit 4 months agopypi sdrf-pipelines} Downloads
Mokapot ⭐ 31
Fast and flexible semi-supervised learning for peptide detection in Python
dependent packages 5total releases 26latest release September 11, 2023most recent commit 6 months agopypi mokapot} Downloads
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