Repositories list

• big-data-biology_org

  Public
  Elm

  •18•0•0•4•Updated Jul 30, 2025Jul 30, 2025

• argNorm

  Public
  ARG normalization by mapping to the ARO ontology.

  antibiotic-resistancebioinformatics

  Python

  •

  MIT License

  •7•58•3•0•Updated Jul 30, 2025Jul 30, 2025

• AEMB_benchmark

  Public
  Python

  •1•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• magsview

  Public
  Elm

  •

  MIT License

  •2•0•0•0•Updated Jul 20, 2025Jul 20, 2025

• SPIREpy

  Public
  Python

  •

  MIT License

  •2•0•1•0•Updated Jul 14, 2025Jul 14, 2025

• macrel

  Public
  Predict AMPs in (meta)genomes and peptides

  bioinformaticsgenomicsbiology+ 3metagenomicsnglesspeptide

  Python

  •

  Other

  •12•83•0•0•Updated Jun 19, 2025Jun 19, 2025

• sardyne

  Public
  Python

  •

  MIT License

  •2•5•0•0•Updated Jun 3, 2025Jun 3, 2025

• ENA_microbial_submission

  Public
  Set of scripts and instructions to upload sequencing reads to the ENA.

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 17, 2025Apr 17, 2025

• SemiBin

  Public
  SemiBin: metagenomics binning with self-supervised deep learning

  bioinformaticsdeep-learningmetagenomics+ 2self-supervised-learningassembly-binning

  Python

  •12•137•21•1•Updated Mar 21, 2025Mar 21, 2025

• VideoTutorials

  Public
  Supporting material for YouTube tutorials

  pythonbioinformaticstutorials+ 1microbiome

  Python

  •1•1•0•0•Updated Mar 17, 2025Mar 17, 2025

• argNorm_benchmark

  Public
  Benchmark repo for argNorm

  Python

  •2•2•0•2•Updated Mar 5, 2025Mar 5, 2025

• SantosJunior_Torres_2024_AMPSphere_v1

  Public
  Figures and files used in the AMPSphere manuscript

  Python

  •

  MIT License

  •2•5•0•0•Updated Jan 2, 2025Jan 2, 2025

• GMSC-mapper

  Public
  bioinformaticsmicrobiomegmsc+ 1small-proteins

  Python

  •

  MIT License

  •4•8•0•1•Updated Nov 26, 2024Nov 26, 2024

• GMSC_website

  Public
  GMSC Frontend

  bioinformaticsmicrobiomegmsc+ 1small-proteins

  Elm

  •

  MIT License

  •2•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• AMPSphereFrontend

  Public
  Bikeshed

  •4•0•0•0•Updated Sep 21, 2024Sep 21, 2024

• Duan2024__GMSCv1_Construction_And_Analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jul 28, 2024Jul 28, 2024

• AMPSphereBackend

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

• GMSC-api

  Public
  bioinformaticsgmscsmall-proteins

  Python

  •2•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• BigDataBiology.markdown_manuscript

  Public
  Simple template for BDB-Lab manuscripts

  TeX

  •

  MIT License

  •1•0•0•0•Updated May 28, 2024May 28, 2024

• talk-tips-n-tricks-large-python

  Public
  Tips & tricks for large scale processing with Python

  HTML

  •5•1•0•0•Updated May 8, 2024May 8, 2024

• co-args

  Public
  Python

  •

  MIT License

  •0•4•0•0•Updated Apr 30, 2024Apr 30, 2024

• SemiBin_tutorial

  Public
  1•1•0•0•Updated Apr 19, 2024Apr 19, 2024

• long-read-magic

  Public
  A website to visualise and download MAGs obtained from long read sequencing.

  BrighterScript

  •

  Other

  •6•0•0•0•Updated Mar 25, 2024Mar 25, 2024

• SemiBin_benchmark

  Public
  Python

  •

  MIT License

  •2•3•0•0•Updated Mar 21, 2024Mar 21, 2024

• SemiBin2_benchmark

  Public
  Python

  •

  MIT License

  •0•6•0•0•Updated Mar 21, 2024Mar 21, 2024

• arg-compare

  Public
  Python

  •3•2•0•0•Updated Feb 5, 2024Feb 5, 2024

• fasta_reader

  Public
  Python

  •1•1•0•0•Updated Dec 5, 2023Dec 5, 2023

• macrel2020benchmark

  Public archive
  Python

  •1•0•0•0•Updated Nov 12, 2022Nov 12, 2022

• AMPSphereWebsite

  Public archive
  Website for global antimicrobial peptides.

  websiteantimicrobial-peptides

  MIT License

  •2•1•6•0•Updated Nov 7, 2022Nov 7, 2022

• quick_amr_db_harmonisation

  Public
  Quick dirty way of mapping ResFinder(FG), DeepARG, SARG, and NCBI AMR databases to CARD's ARO

  Python

  •

  GNU General Public License v3.0

  •2•1•1•0•Updated May 31, 2022May 31, 2022