Skip to content

@AbeelLab AbeelLab

Change the repository type filter

All

    Repositories list

    60 repositories

    • atk

      Public
      Abeel Toolkit is set of utility classes that are used in our other projects.
      Java
      •
      Other
      •1•1•0•0•Updated Feb 23, 2026Feb 23, 2026

    • Comparative-Microbial-Network-Analysis

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • ml-assisted-p-coumaric-acid-optimization

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • BenchmarkProjectDSMF

      Public
      Comparing recommendation strategies for simulated DBTL cycles
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • drought-microbiome-analysis

      Public
      A collection of processed datasets and a QIIME2-based pipeline to analyze microbiome data from plant roots and soil
      Python
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • jaxkineticmodel

      Public
      Building, simulating, and training systems biology models using JAX/Diffrax
      systems-biologydynamical-systemskinetic-modeling
      systems-biologydynamical-systemskinetic-modelingneural-odes
      Jupyter Notebook
      •
      Apache License 2.0
      •0•8•0•0•Updated Nov 24, 2025Nov 24, 2025

    • VB2_network_analysis

      Public
      Comparative analysis of microbial association networks in response to Vitamin B2 (VB2) supplementation.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • tudelft-report-thesis-template

      Public template
      A LaTeX report/thesis template that aims to simplify and improve the (Xe)LaTeX template provided by the TU Delft. Ready-to-go with its rewritten class file and …
      TeX
      •22•0•0•0•Updated Oct 7, 2025Oct 7, 2025

    • simulated-dbtl

      Public
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Mar 14, 2025Mar 14, 2025

    • safpred

      Public
      Synteny-aware gene function prediction for bacteria using protein embeddings
      Python
      •2•5•1•0•Updated Jan 8, 2025Jan 8, 2025

    • SAFPredDB

      Public
      Bacterial synteny database
      Python
      •1•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • multi_meta_omics

      Public
      Reprodubility scripts for an ML pipeline for meta-omics data prediction
      Python
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • poultry_cecum_response

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • abaumannii-pangenome

      Public
      Python
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • RP2023_kirbeyi

      Public
      Research Project 2023-2024 Q2 - Kirbeyi
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 28, 2024Jan 28, 2024

    • RP2023_Jarosz

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 28, 2024Jan 28, 2024

    • RP2023_Alwani

      Public
      Contains the PPCA, VAE and CVAE model used for the research project. Aside from this there are separate folders for research documents and the dataset related t…
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jan 28, 2024Jan 28, 2024

    • SHIP

      Public
      Python
      •
      GNU General Public License v3.0
      •1•6•2•0•Updated Jan 18, 2024Jan 18, 2024

    • quanttb

      Public
      QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.
      Python
      •
      GNU General Public License v3.0
      •5•7•0•3•Updated Jul 6, 2023Jul 6, 2023

    • javaml

      Public
      Java Machine Learning Library
      Java
      •20•62•3•1•Updated Jul 3, 2023Jul 3, 2023

    • long-read-assembly-benchmark

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 27, 2023Jan 27, 2023

    • hat

      Public
      Haplotype Assembly Tool
      Python
      •
      GNU General Public License v3.0
      •2•8•0•0•Updated Jul 11, 2022Jul 11, 2022

    • GraphClean

      Public
      Assembly graph cleaning through machine learning improves de novo long-read assembly
      Python
      •2•0•0•1•Updated Jun 21, 2022Jun 21, 2022

    • vlpb-assembly-workshop

      Public
      1•0•0•0•Updated Jun 8, 2022Jun 8, 2022

    • abeellab.github.io

      Public
      HTML
      •0•0•0•0•Updated Mar 30, 2022Mar 30, 2022

    • ctag

      Public
      Graph genome browser
      Java
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 10, 2022Mar 10, 2022

    • cs4255

      Public
      Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft
      1•2•0•0•Updated Nov 5, 2020Nov 5, 2020

    • ptolemy

      Public
      Scala
      •
      GNU General Public License v3.0
      •2•10•5•0•Updated Jul 23, 2020Jul 23, 2020

    • redwood2

      Public
      1•0•0•0•Updated Jun 12, 2020Jun 12, 2020

    • graphlift

      Public
      1•0•0•0•Updated Apr 2, 2020Apr 2, 2020