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@leylabmpi

Department of Microbiome Science at the MPI for Biology

Popular repositories Loading

  1. Struo2 Struo2 Public

    Scalable creating/updating of metagenome profiling databases

    Jupyter Notebook 62 9

  2. Struo Struo Public

    Ley Lab MetaGenome Profiler DataBase generator

    Jupyter Notebook 49 4

  3. SynTracker SynTracker Public

    SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same species) using genome synteny.

    Python 37 6

  4. DeepMAsED DeepMAsED Public

    Deep learning for Metagenome Assembly Error Detection

    Jupyter Notebook 25 5

  5. pyTecanFluent pyTecanFluent Public

    Python interface to TECAN Fluent liquid handling robot

    Python 21 2

  6. endoR endoR Public

    Code and manual of the endoR R-package (Ruaud et al, in preparation).

    Jupyter Notebook 12

Repositories

Showing 10 of 53 repositories
  • StrainVis Public

    A Python-based web application for interactive visual analysis of strain-tracking methods

    leylabmpi/StrainVis’s past year of commit activity
    Python 1 0 0 0 Updated Nov 13, 2025
  • SynTrackerVis Public

    SynTrackerVis: a Python-based web application for interactive visual analysis of SynTracker's results

    leylabmpi/SynTrackerVis’s past year of commit activity
    Python 0 1 0 1 Updated Nov 13, 2025
  • FlaPro Public
    leylabmpi/FlaPro’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Nov 5, 2025
  • SynTracker Public

    SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same species) using genome synteny.

    leylabmpi/SynTracker’s past year of commit activity
    Python 37 6 0 7 Updated Sep 17, 2025
  • sel_trans_behavior Public

    Essential code of the Suzuki, T. et al "Selection and transmission of the gut microbiome alone can shift mammalian behavior" publication.

    leylabmpi/sel_trans_behavior’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 1 0 0 Updated Sep 3, 2025
  • global-methanogen-strain-diversity Public

    R notebooks and data for strain-level and pangenome analysis of human gut methanogens based on metagenomic and isolate genome sequencing across diverse populations

    leylabmpi/global-methanogen-strain-diversity’s past year of commit activity
    0 0 0 0 Updated Jul 11, 2025
  • Struo2 Public

    Scalable creating/updating of metagenome profiling databases

    leylabmpi/Struo2’s past year of commit activity
    Jupyter Notebook 62 MIT 9 19 0 Updated Jun 25, 2025
  • TUK_db_shiny Public

    Shiny db viewer for TUK data

    leylabmpi/TUK_db_shiny’s past year of commit activity
    R 0 0 0 0 Updated Jun 11, 2025
  • shortbred Public Forked from biobakery/shortbred

    ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

    leylabmpi/shortbred’s past year of commit activity
    Python 0 7 0 0 Updated Jun 1, 2025
  • LeyLabRMisc Public

    R package of Ley Lab misc functions, rmd templates, etc.

    leylabmpi/LeyLabRMisc’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 3 0 1 Updated May 22, 2025
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