All

53 repositories

FlaPro
Public
Jupyter Notebook
•2•0•0•0•Updated May 21, 2026May 21, 2026
StrainVis
Public
A Python-based web application for interactive visual analysis of strain-tracking methods
Python
•0•4•0•0•Updated May 18, 2026May 18, 2026
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 populati…
Python
•0•0•0•0•Updated Mar 4, 2026Mar 4, 2026
uHEAT
Public
R code for analysis presented in the uHEAT manuscript
R
•0•0•0•0•Updated Feb 19, 2026Feb 19, 2026
SynTrackerVis
Public
SynTrackerVis: a Python-based web application for interactive visual analysis of SynTracker's results
Python
•0•0•0•0•Updated Nov 13, 2025Nov 13, 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…
Python
•8•41•0•7•Updated Sep 17, 2025Sep 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.
Jupyter Notebook
•
GNU General Public License v3.0
•2•0•0•0•Updated Sep 3, 2025Sep 3, 2025
Struo2
Public
Scalable creating/updating of metagenome profiling databases
database pipeline ngs
database pipeline ngs metagenomics
Jupyter Notebook
•
MIT License
•8•62•19•0•Updated Jun 25, 2025Jun 25, 2025
TUK_db_shiny
Public
Shiny db viewer for TUK data
shiny-apps
shiny-apps
R
•0•0•0•0•Updated Jun 11, 2025Jun 11, 2025
shortbred
Public
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…
Python
•
Other
•7•0•0•0•Updated Jun 1, 2025Jun 1, 2025
LeyLabRMisc
Public
R package of Ley Lab misc functions, rmd templates, etc.
r utilities r-packages
r utilities r-packages
Jupyter Notebook
•
GNU General Public License v3.0
•3•1•0•1•Updated May 22, 2025May 22, 2025
qiime_2_ll_quick_viewer
Public
qiime2
qiime2
Python
•
MIT License
•2•3•0•14•Updated Aug 13, 2024Aug 13, 2024
ll_pipeline_utils
Public
Utility scripts for running Ley Lab pipelines
utils-repo ll-pipeline
utils-repo ll-pipeline
Python
•0•1•0•0•Updated Jun 12, 2024Jun 12, 2024
resmico
Public
Identifying misassemblies via deep learning
bioinformatics deep-learning metagenomics
bioinformatics deep-learning metagenomics metagenome-assembly
Jupyter Notebook
•
MIT License
•1•11•8•0•Updated May 1, 2024May 1, 2024
Synteny_analyses
Public
R
•0•0•0•0•Updated Apr 22, 2024Apr 22, 2024
pyTecanFluent
Public
Python interface to TECAN Fluent liquid handling robot
python python-packages liquid-automation
python python-packages liquid-automation
Python
•
MIT License
•2•21•0•0•Updated Apr 18, 2024Apr 18, 2024
Schoen_Christensenella_2023
Public
HTML
•0•0•0•0•Updated Nov 11, 2023Nov 11, 2023
endoR
Public
Code and manual of the endoR R-package (Ruaud et al, in preparation).
data-science machine-learning random-forest
data-science machine-learning random-forest r-packages
Jupyter Notebook
•
GNU General Public License v3.0
•0•11•0•0•Updated Oct 12, 2023Oct 12, 2023
Col_OB_CHS
Public
Code for analysis of metagenomes of Colombian adults in OB and CHS
R
•1•1•0•0•Updated May 3, 2023May 3, 2023
SynTracker_old
Public
0•0•1•0•Updated Apr 11, 2023Apr 11, 2023
global_metagenome_diversity
Public
Global human gut metagenome diversity study: code and notes
machine-learning research-project diversity-measures
machine-learning research-project diversity-measures
Jupyter Notebook
•0•1•0•0•Updated Feb 6, 2023Feb 6, 2023
Struo
Public
Ley Lab MetaGenome Profiler DataBase generator
database pipeline ngs
database pipeline ngs metagenomics
Jupyter Notebook
•
MIT License
•4•48•1•0•Updated Nov 9, 2022Nov 9, 2022
CoreGenomePrimers
Public
Design clade-specific primers targeting a pan-genome core gene
bioinformatics bacteria primer-design
bioinformatics bacteria primer-design archaea primers
Jupyter Notebook
•
MIT License
•1•2•1•0•Updated Oct 10, 2022Oct 10, 2022
silent_flagellins
Public
Code associated to the silent recognition of flagellins by Toll-like receptor 5 paper
research-project
research-project
Jupyter Notebook
•0•0•0•0•Updated Oct 5, 2022Oct 5, 2022
RTecanFluentShiny
Public
R interface to TECAN Fluent liquid handling robot
shiny-apps
shiny-apps
R
•
MIT License
•0•1•0•0•Updated Aug 16, 2022Aug 16, 2022
sgepy
Public
sge job-submission high-perofrmance-computing
sge job-submission high-perofrmance-computing
Python
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
pseudomonas_maize_genome
Public archive
research-project
research-project
Python
•
MIT License
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
MicrobeMeter
Public
shiny-apps
shiny-apps
R
•
MIT License
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
alphafold_sm
Public
snakemake-pipelines alphafold2
snakemake-pipelines alphafold2
Python
•
MIT License
•0•0•0•0•Updated Aug 9, 2022Aug 9, 2022
MGSIM
Public
simulations genomes metagenomes
simulations genomes metagenomes
Python
•
MIT License
•0•0•0•0•Updated Aug 9, 2022Aug 9, 2022

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Department of Microbiome Science at the MPI for Biology

All

All

53 repositories

FlaPro

StrainVis

global-methanogen-strain-diversity

uHEAT

SynTrackerVis

SynTracker

sel_trans_behavior

Struo2

TUK_db_shiny

shortbred

LeyLabRMisc

qiime_2_ll_quick_viewer

ll_pipeline_utils

resmico

Synteny_analyses

pyTecanFluent

Schoen_Christensenella_2023

endoR

Col_OB_CHS

SynTracker_old

global_metagenome_diversity

Struo

CoreGenomePrimers

silent_flagellins

RTecanFluentShiny

sgepy

pseudomonas_maize_genome

MicrobeMeter

alphafold_sm

MGSIM

All

All

Repositories list

53 repositories