Repositories list

• xtracer

  Public
  Converting PAMAF .mbi data to pseudo-MS/MS files by untargeted methods.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• full_dia

  Public
  Full-DIA is an open source software for diaPASEF data analysis that leverages deep learning to improve proteome coverage, quantitative accuracy and analysis spe…

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•33 stars•11 issue•00 pull requests•Updated May 7, 2026May 7, 2026

• AI-robotics-proteomics

  Public
  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• scTransient

  Public
  Detection of transient events in single-cell data.

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• odda

  Public
  Omics Data Discovery Agents

  Shell

  •

  GNU General Public License v3.0

  •33 forks•1212 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• request_visualization

  Public
  Visualization tool for examining feature requests made by ODDA agents.

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• odda_utils

  Public
  Utilities for Omics Data Discovery Agents

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• odda_thermofisher

  Public
  Exposes tools for handling ThermoFisher files and converting them to different formats.

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• odda_maxquant

  Public
  Apptainer definition files and build scripts for MCP access to MaxQuant

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• odda_diann

  Public
  Apptainer definition files and build scripts for MCP access to DIA-NN

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• scTransient_notebooks

  Public
  Notebooks for the analysis of data related to the scTransient publication.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• generation_of_iNeurons

  Public
  Extended NGN2 Expression in iPSCs Dramatically Enhances Purity of Neuronal Cultures

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 30, 2026Jan 30, 2026

• Retinal_Alzheimer_Prediction

  Public
  Code related to the prediction of Alzheimer's disease and related measures.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Dec 22, 2025Dec 22, 2025

• ClaudeCode_with_Azure

  Public
  Instructions for getting Claude Code to work using models deployed on Azure.

  GNU General Public License v3.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Dec 17, 2025Dec 17, 2025

• ubiquitin_ad

  Public
  Notebooks containing analyses for the ubiquitin-related AD project.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• ProteomicsAnalyzer-Data

  Public
  Data to accompany the proteomics-analyzer example vibe coded application

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 21, 2025Nov 21, 2025

• ProteomicsAnalyzer

  Public
  Vibe coded proteomic data analysis streamlit app

  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 10, 2025Oct 10, 2025

• SMAD-project

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2025Aug 20, 2025

• articles-to-code

  Public
  On-Demand Generation of Core Algorithms from Scientific Publications

  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jul 28, 2025Jul 28, 2025

• AttentionSmithy

  Public
  Modular toolkit for rapidly building and customizing transformer architectures.

  Python

  •

  MIT License

  •22 forks•99 stars•00 issues•11 pull request•Updated Jul 8, 2025Jul 8, 2025

• pscs

  Public
  Platform for Single-Cell Science

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•11 star•3333 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• pscs_api

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• DImeta

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 24, 2025Jun 24, 2025

• hepg2_abc

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 19, 2025Jun 19, 2025

• pscs_scanpy

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2025May 29, 2025

• typomancy

  Public
  Toolkit for converting HTML string input into Python types indicated by TypeHints

  htmlflaskjson+ 2

  htmlflaskjsonpython3typehint

  Python

  •

  MIT License

  •00 forks•11 star•22 issues•00 pull requests•Updated May 29, 2025May 29, 2025

• scTransientNotebooks

  Public
  Notebooks connected to scTransient publication for processing data.

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated May 8, 2025May 8, 2025

• geneformer

  Public
  A recreation of the geneformer model using AttentionSmithy

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 4, 2025May 4, 2025

• machine-translation

  Public
  Replication of the "Attention Is All you Need" machine translation model using AttentionSmithy.

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•22 pull requests•Updated Apr 25, 2025Apr 25, 2025

• Medication-BG-alteration

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025