Mann Labs

CKG

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

alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.

alphapeptdeep

Deep learning framework for proteomics

alphatims

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.

alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.

alphapeptstats

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

directlfq

Fast and accurate label-free quantification for small and very large numbers of proteomes

alphaviz

AlphaViz is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with Bruker instrument.

OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

structuremap

Python package for investigating the structural context of PTMs

alphabase

Infrastructure of AlphaX ecosystem

timsrust

pydiaid

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.

PeptDeep-HLA

DL model to predict HLA peptide presentation

alpharaw

An open-source Python package to unify raw MS data accession and storage.

SPARCSpy

structuremap_analysis

Analysis workflow for investigating the structural context of PTMs

py-lmd

DeepScore

The DeepScore Repository for the EuBIC 2023 Hackathon

SPARCStools

python tools to perform data parsing and image stitching on microscopy data

Quality-Control-of-the-Plasma-Proteome

single-cell-DVP

refquant

Reference-channel based quantification for mDIA data

alphasynchro

ReactomeGSApython

Python interface to Reactome's gene set enrichment analysis service

timspeak

MitoPhos

MitoPhos data analysis notebooks

slurm_scripts

SPARCS_pub_figures

Notebook and data to recreate figures from SPARCS manuscript

streamlit_peptide_overlay

An example streamlit application that allows plotting on a protein sequence.