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alphabase

Infrastructure of AlphaX ecosystem

alphamap

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

alphapept

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

alphapeptdeep

Deep learning framework for proteomics

alphapeptstats

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

alpharaw

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

alphasynchro

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.

alphaviz

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

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

cyclingproximityanalysis

deepcollisionalcrosssection

deepscore

The DeepScore Repository for the EuBIC 2023 Hackathon

directlfq

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

identipy_server_dockerize

A docker container for building and running the Identipy Server application https://bitbucket.org/levitsky/identipy_server/src

mini_proteindb

A small demo of how to use sqlite in python and BioPy to read fasta files and put them in databases.

mitophos

MitoPhos data analysis notebooks

ms_booker

A simple web app for booking mass spec machines

omiclearn

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

peptdeep-hla

DL model to predict HLA peptide presentation

perseusr-spatialdistance

Training/template code for PerseusR plugins on the example of profile distance calculation

proteomesoflife

python based queries for the proteomesoflife neo4j network database

proteomicsvisualization

This is a collection of minimal code to visualize various aspects of proteomics data.

py-lmd

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.

quality-control-of-the-plasma-proteome

reactomegsapython

Python interface to Reactome's gene set enrichment analysis service

refquant

Reference-channel based quantification for mDIA data

single-cell-dvp

slurm_scripts