Mann Labs

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44 repositories

alpharaw
Public
An open-source Python package to unify raw MS data accession and storage.
data-storage mass-spectrometry raw-data data-accession
Jupyter Notebook
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Apache License 2.0
•5•21•8•0•Updated Mar 25, 2025Mar 25, 2025
scPortrait
Public
scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
python imaging single-cell-analysis single-cell-images
Python
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Apache License 2.0
•3•42•20•1•Updated Mar 25, 2025Mar 25, 2025
alphapeptstats
Public
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
proteomics mass-spectrometry maxquant dia-nn fragpipe alphapept-ecosystem spectronaut msfragger
Jupyter Notebook
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Apache License 2.0
•16•66•23•14•Updated Mar 25, 2025Mar 25, 2025
alphapeptdeep
Public
Deep learning framework for proteomics
proteomics hla python machine-learning deep-learning
Jupyter Notebook
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Apache License 2.0
•22•121•25•2•Updated Mar 24, 2025Mar 24, 2025
alphaquant
Public
An open-source Python package for accurate and sensitive peptide and protein quantification.
bioinformatics proteomics dia mass-spectrometry quantification tmt lfq
Python
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Apache License 2.0
•1•13•5•1•Updated Mar 23, 2025Mar 23, 2025
refquant
Public
Reference-channel based quantification for mDIA data
Jupyter Notebook
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Apache License 2.0
•2•4•1•1•Updated Mar 22, 2025Mar 22, 2025
directlfq
Public
Fast and accurate label-free quantification for small and very large numbers of proteomes
python bioinformatics algorithms proteomics quantification alphapept-ecosystem
Jupyter Notebook
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Apache License 2.0
•5•48•6•2•Updated Mar 22, 2025Mar 22, 2025
alphabase
Public
Infrastructure of AlphaX ecosystem
python infrastructure proteomics mass-spectrometry
Jupyter Notebook
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Apache License 2.0
•9•37•9•6•Updated Mar 22, 2025Mar 22, 2025
alphadia
Public
modular & open DIA search
open-source bioinformatics proteomics mass-spectrometry peptide-identification
Jupyter Notebook
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Apache License 2.0
•5•65•22•9•Updated Mar 22, 2025Mar 22, 2025
scPortrait-notebooks
Public
Jupyter Notebook
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Apache License 2.0
•0•2•0•1•Updated Mar 20, 2025Mar 20, 2025
alphamap
Public
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
gui proteomics mass-spectrometry peptide-level visualization python
Jupyter Notebook
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Apache License 2.0
•19•81•17•5•Updated Mar 19, 2025Mar 19, 2025
alphashared
Public
Shared non-production code for AlphaX packages
Python
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Apache License 2.0
•2•2•0•2•Updated Mar 19, 2025Mar 19, 2025
alphatims
Public
An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.
python cli gui dia dda mass-spectrometry ms ion-mobility tof max-planck-institute
Python
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Apache License 2.0
•28•86•2•7•Updated Mar 13, 2025Mar 13, 2025
py-lmd
Public
Read, create and write cutting data for the Leica LMD6 & LMD7 microscope. Build reproducible workflows to calibrate, import SVG files and convert single-cell segmentation masks.
Python
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MIT License
•1•8•6•0•Updated Feb 28, 2025Feb 28, 2025
alphaviz
Public
AlphaViz is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with Bruker instrument.
visualization quality-control mass-spectrometry bruker
Python
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Apache License 2.0
•2•32•10•0•Updated Feb 18, 2025Feb 18, 2025
pydiaid
Public
An open-source Python package for dia-PASEF methods with Automated Isolation Design (py_diAID) from the Mann Labs at the Max Planck Institute of Biochemistry.
Jupyter Notebook
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Apache License 2.0
•5•19•9•0•Updated Feb 12, 2025Feb 12, 2025
timsrust
Public
Rust
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Apache License 2.0
•11•25•2•1•Updated Feb 3, 2025Feb 3, 2025
structuremap
Public
Python package for investigating the structural context of PTMs
Jupyter Notebook
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Apache License 2.0
•10•28•2•0•Updated Jan 9, 2025Jan 9, 2025
SPARCStools
Public
python tools to perform data parsing and image stitching on microscopy data
Jupyter Notebook
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MIT License
•2•6•3•0•Updated Aug 5, 2024Aug 5, 2024
alphasynchro
Public
Python
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Apache License 2.0
•0•2•0•0•Updated Jul 8, 2024Jul 8, 2024
OmicLearn
Public
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
machine-learning bioinformatics proteomics omics transcriptomics biomarker-discovery
Python
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Other
•19•33•2•0•Updated Jun 10, 2024Jun 10, 2024
SPARCSpy
Public
Jupyter Notebook
•6•11•9•0•Updated May 31, 2024May 31, 2024
alphapept
Public
A modular, python-based framework for mass spectrometry. Powered by nbdev.
bioinformatics proteomics mass-spectrometry alphapept-ecosystem
HTML
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Apache License 2.0
•31•176•21•5•Updated Apr 19, 2024Apr 19, 2024
PeptDeep-HLA
Public
DL model to predict HLA peptide presentation
hla peptidomics immunopeptidomics deep-learning
Jupyter Notebook
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Apache License 2.0
•6•14•1•0•Updated Jan 31, 2024Jan 31, 2024
structuremap_analysis
Public
Analysis workflow for investigating the structural context of PTMs
Jupyter Notebook
•6•11•3•0•Updated Jan 8, 2024Jan 8, 2024
SPARCS_pub_figures
Public
Notebook and data to recreate figures from SPARCS manuscript
Jupyter Notebook
•0•2•0•0•Updated Jan 1, 2024Jan 1, 2024
MitoPhos
Public
MitoPhos data analysis notebooks
Jupyter Notebook
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Apache License 2.0
•0•1•0•0•Updated Nov 20, 2023Nov 20, 2023
timspeak
Public
Python
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Apache License 2.0
•0•2•1•0•Updated Oct 5, 2023Oct 5, 2023
slurm_scripts
Public
Shell
•1•1•0•0•Updated Sep 12, 2023Sep 12, 2023
single-cell-DVP
Public
Jupyter Notebook
•1•9•0•0•Updated Jun 1, 2023Jun 1, 2023