Mann Labs

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43 repositories

alphadia
Public
modular & open DIA search
open-source bioinformatics proteomics mass-spectrometry peptide-identification
Jupyter Notebook
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Apache License 2.0
•3•56•17•10•Updated Dec 23, 2024Dec 23, 2024
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
•15•61•20•11•Updated Dec 23, 2024Dec 23, 2024
scPortrait
Public
Python
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Apache License 2.0
•1•35•24•3•Updated Dec 21, 2024Dec 21, 2024
alphabase
Public
Infrastructure of AlphaX ecosystem
python infrastructure proteomics mass-spectrometry
Jupyter Notebook
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Apache License 2.0
•10•32•9•18•Updated Dec 20, 2024Dec 20, 2024
alphashared
Public
Shared non-production code for AlphaX packages
Python
•0•0•0•0•Updated Dec 20, 2024Dec 20, 2024
py-lmd
Public
Jupyter Notebook
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MIT License
•1•8•7•2•Updated Dec 19, 2024Dec 19, 2024
timsrust
Public
Rust
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Apache License 2.0
•11•24•3•1•Updated Dec 19, 2024Dec 19, 2024
scPortrait-notebooks
Public
Jupyter Notebook
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Apache License 2.0
•0•2•0•1•Updated Dec 17, 2024Dec 17, 2024
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
•26•82•5•11•Updated Dec 17, 2024Dec 17, 2024
alphapeptdeep
Public
Deep learning framework for proteomics
proteomics hla python machine-learning deep-learning
Jupyter Notebook
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Apache License 2.0
•24•113•24•3•Updated Dec 10, 2024Dec 10, 2024
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
•4•19•9•0•Updated Nov 29, 2024Nov 29, 2024
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•43•8•1•Updated Nov 26, 2024Nov 26, 2024
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
•18•77•17•9•Updated Nov 8, 2024Nov 8, 2024
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
•3•18•7•0•Updated Sep 17, 2024Sep 17, 2024
SPARCStools
Public
python tools to perform data parsing and image stitching on microscopy data
Jupyter Notebook
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MIT License
•2•5•4•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•32•2•0•Updated Jun 10, 2024Jun 10, 2024
SPARCSpy
Public
Jupyter Notebook
•6•9•9•0•Updated May 31, 2024May 31, 2024
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•30•10•0•Updated Apr 24, 2024Apr 24, 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
•30•170•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•13•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
structuremap
Public
Python package for investigating the structural context of PTMs
Jupyter Notebook
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Apache License 2.0
•9•28•2•1•Updated Jan 8, 2024Jan 8, 2024
SPARCS_pub_figures
Public
Notebook and data to recreate figures from SPARCS manuscript
Jupyter Notebook
•0•1•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
refquant
Public
Reference-channel based quantification for mDIA data
Jupyter Notebook
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Apache License 2.0
•1•4•1•0•Updated Sep 8, 2023Sep 8, 2023
single-cell-DVP
Public
Jupyter Notebook
•0•8•0•0•Updated Jun 1, 2023Jun 1, 2023
streamlit_peptide_overlay
Public
An example streamlit application that allows plotting on a protein sequence.
Python
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Apache License 2.0
•0•0•0•0•Updated Mar 28, 2023Mar 28, 2023