Skip to content

@xomicsdatascience Multiomics + Data Science Lab

Change the repository type filter

All

    Repositories list

    38 repositories

    • scTransient_notebooks

      Public
      Notebooks for the analysis of data related to the scTransient publication.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 6, 2026Feb 6, 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
      •0•2•0•0•Updated Feb 4, 2026Feb 4, 2026

    • generation_of_iNeurons

      Public
      Extended NGN2 Expression in iPSCs Dramatically Enhances Purity of Neuronal Cultures
      Jupyter Notebook
      •1•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • xtracer

      Public
      Converting PAMAF .mbi data to pseudo-MS/MS files by untargeted methods.
      Python
      •0•0•0•0•Updated Jan 15, 2026Jan 15, 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
      •0•0•1•0•Updated Dec 22, 2025Dec 22, 2025

    • scTransient

      Public
      Detection of transient events in single-cell data.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • ClaudeCode_with_Azure

      Public
      Instructions for getting Claude Code to work using models deployed on Azure.
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 17, 2025Dec 17, 2025

    • ProteomicsAnalyzer-Data

      Public
      Data to accompany the proteomics-analyzer example vibe coded application
      Jupyter Notebook
      •0•1•0•0•Updated Nov 21, 2025Nov 21, 2025

    • ProteomicsAnalyzer

      Public
      Vibe coded proteomic data analysis streamlit app
      Python
      •0•3•0•0•Updated Oct 10, 2025Oct 10, 2025

    • SMAD-project

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • articles-to-code

      Public
      On-Demand Generation of Core Algorithms from Scientific Publications
      Jupyter Notebook
      •0•3•0•0•Updated Jul 28, 2025Jul 28, 2025

    • AttentionSmithy

      Public
      Modular toolkit for rapidly building and customizing transformer architectures.
      Python
      •
      MIT License
      •3•7•0•1•Updated Jul 8, 2025Jul 8, 2025

    • pscs

      Public
      Platform for Single-Cell Science
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•33•0•Updated Jul 1, 2025Jul 1, 2025

    • pscs_api

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•2•0•Updated Jul 1, 2025Jul 1, 2025

    • DImeta

      Public
      Python
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • hepg2_abc

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • pscs_scanpy

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 29, 2025May 29, 2025

    • typomancy

      Public
      Toolkit for converting HTML string input into Python types indicated by TypeHints
      htmlflaskjsonpython3typehint
      Python
      •
      MIT License
      •0•1•2•0•Updated May 29, 2025May 29, 2025

    • scTransientNotebooks

      Public
      Notebooks connected to scTransient publication for processing data.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 8, 2025May 8, 2025

    • geneformer

      Public
      A recreation of the geneformer model using AttentionSmithy
      Python
      •
      MIT License
      •1•0•0•0•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
      •0•1•0•2•Updated Apr 25, 2025Apr 25, 2025

    • Medication-BG-alteration

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • trajectory_review

      Public
      A repository for storing notebooks working through considerations relevant for trajectory inference.
      Jupyter Notebook
      •0•1•0•0•Updated Feb 12, 2025Feb 12, 2025

    • RnaToProteinDataModule

      Public
      Classes for loading transcriptome and proteome data for deep learning model training.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 29, 2025Jan 29, 2025

    • Single-Cell-Storage

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jan 21, 2025Jan 21, 2025

    • FAIMS_MachineLearning

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • subgroup_example2

      Public
      Other
      Python
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • subgroup_example

      Public
      Adding remote repository
      0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • transcriptome-proteome-nas-manubot

      Public
      HTML
      •
      Creative Commons Attribution 4.0 International
      •0•5•5•0•Updated Nov 11, 2024Nov 11, 2024

    • faims

      Public
      Flask app for FAIMS CV paper
      Python
      •0•0•5•0•Updated Sep 11, 2024Sep 11, 2024