Repositories list

• cayman

  Public
  A command-line tool for profiling CAZyme abundances in metagenomic datasets.

  Python

  •

  MIT License

  •4•14•1•0•Updated Dec 9, 2025Dec 9, 2025

• CHAMOIS

  Public
  Chemical Hierarchy Approximation for secondary Metabolism clusters Obtained In Silico.

  HTML

  •

  GNU General Public License v3.0

  •1•7•0•0•Updated Dec 7, 2025Dec 7, 2025

• GECCO

  Public
  GEne Cluster prediction with COnditional random fields.

  pythonbioinformaticsgenomics+ 4metagenomicssecondary-metabolitesnatural-productsbiosynthetic-gene-clusters

  Python

  •

  GNU General Public License v3.0

  •8•76•7•0•Updated Nov 26, 2025Nov 26, 2025

• ZellerLab.github.io

  Public
  Website for the Zeller Lab

  HTML

  •44•1•4•0•Updated Nov 21, 2025Nov 21, 2025

• ds-iai

  Public
  R

  •0•0•0•0•Updated Oct 28, 2025Oct 28, 2025

• cayman_paper

  Public
  R

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• gut-microbial-metabolism-of-immunosuppressants

  Public
  R

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jul 28, 2025Jul 28, 2025

• crc-meta-ii

  Public
  R

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

• IGUA

  Public
  Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.

  Python

  •

  GNU General Public License v3.0

  •1•14•0•0•Updated May 20, 2025May 20, 2025

• SIMBA

  Public
  R package for the simulation of metagenomic samples

  R

  •2•2•4•0•Updated Mar 31, 2025Mar 31, 2025

• stag

  Public
  A hierarchical taxonomic classifier for metagenomic sequences

  microbiomesequence-classification

  Python

  •2•8•11•1•Updated Nov 30, 2024Nov 30, 2024

• nevermore

  Public
  Zeller-group fork of Nevermore

  Nextflow

  •

  MIT License

  •1•1•2•0•Updated Nov 8, 2024Nov 8, 2024

• An-Atlas-of-the-Liver-Cancer-Microbiome

  Public
  An Atlas of the Liver Cancer Microbiome

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

• BAMBI

  Public
  Benchmarking Analysis of MicroBiome Inference methods

  R

  •1•2•0•0•Updated Aug 23, 2024Aug 23, 2024

• Buchinger_Long_Term_Fasting

  Public
  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated Aug 15, 2024Aug 15, 2024

• vortex_light

  Public
  Nextflow

  •

  MIT License

  •0•1•0•1•Updated May 29, 2024May 29, 2024

• siamcat

  Public
  R package for Statistical Inference of Associations between Microbial Communities And host phenoType

  R

  •15•57•10•1•Updated Jan 30, 2024Jan 30, 2024

• crc_meta

  Public
  Code and analysis results for the CRC shotgun meta-analysis

  R

  •

  GNU General Public License v3.0

  •30•38•0•0•Updated Sep 28, 2022Sep 28, 2022

• commensal_clostridiales

  Public
  Analysis code for the commensal Clostridiales project

  R

  •0•0•0•0•Updated Jul 4, 2022Jul 4, 2022

• GECCO-data

  Public
  The dvc pipeline to build the data for training GECCO.

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 7, 2022Jun 7, 2022

• gaga2

  Public
  Nextflow

  •0•3•2•1•Updated Nov 24, 2021Nov 24, 2021

• specI_utilities

  Public
  usefuls scripts to work with specI clusters

  Python

  •0•0•0•0•Updated Mar 24, 2021Mar 24, 2021

• siamcat_paper

  Public
  Analysis scripts and results presented in the SIAMCAT paper

  R

  •

  GNU General Public License v3.0

  •3•4•0•0•Updated Jan 29, 2021Jan 29, 2021

• EBI_metaG_bioinformatics

  Public
  Materials for the EMBL-EBI Metagenomics Bioinformatics course

  HTML

  •0•0•0•0•Updated Nov 6, 2020Nov 6, 2020

• hd-hub-tools

  Public
  HD-HuB Tool Descriptions

  Python

  •0•0•0•0•Updated Sep 24, 2019Sep 24, 2019

• hd-hub-profiles

  Public
  Profiles of HD-HuB Members

  0•0•0•0•Updated Aug 30, 2019Aug 30, 2019