Department of Microbiome Science at the MPI for Biology

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49 repositories

SynTrackerVis
Public
SynTrackerVis: a Python-based web application for interactive visual analysis of SynTracker's results
Python
•0•0•0•0•Updated Jun 5, 2025Jun 5, 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 metagenomic data and determine the presence and abundance of the protein families of interest.
Python
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Other
•7•0•0•0•Updated Jun 1, 2025Jun 1, 2025
LeyLabRMisc
Public
R package of Ley Lab misc functions, rmd templates, etc.
utilities r-packages r
Jupyter Notebook
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GNU General Public License v3.0
•2•1•0•1•Updated May 22, 2025May 22, 2025
uHEAT
Public
R code for analysis presented in the uHEAT manuscript
R
•0•0•0•0•Updated Feb 19, 2025Feb 19, 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
•7•31•0•7•Updated Feb 3, 2025Feb 3, 2025
qiime_2_ll_quick_viewer
Public
qiime2
Python
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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
Python
•0•1•0•0•Updated Jun 12, 2024Jun 12, 2024
resmico
Public
Identifying misassemblies via deep learning
metagenome-assembly bioinformatics deep-learning metagenomics
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-packages liquid-automation python
Python
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MIT License
•2•19•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).
r-packages data-science machine-learning random-forest
Jupyter Notebook
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GNU General Public License v3.0
•0•12•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•0•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
research-project diversity-measures machine-learning
Jupyter Notebook
•0•1•0•0•Updated Feb 6, 2023Feb 6, 2023
Struo2
Public
Scalable creating/updating of metagenome profiling databases
database pipeline ngs metagenomics
Jupyter Notebook
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MIT License
•8•60•18•0•Updated Jan 22, 2023Jan 22, 2023
Struo
Public
Ley Lab MetaGenome Profiler DataBase generator
database pipeline ngs metagenomics
Jupyter Notebook
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MIT License
•4•50•1•0•Updated Nov 9, 2022Nov 9, 2022
CoreGenomePrimers
Public
Design clade-specific primers targeting a pan-genome core gene
bacteria primer-design archaea primers bioinformatics
Jupyter Notebook
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MIT License
•1•1•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
Jupyter Notebook
•0•0•0•0•Updated Oct 5, 2022Oct 5, 2022
RTecanFluentShiny
Public
R interface to TECAN Fluent liquid handling robot
shiny-apps
R
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MIT License
•0•1•0•0•Updated Aug 16, 2022Aug 16, 2022
sgepy
Public
sge job-submission high-perofrmance-computing
Python
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
pseudomonas_maize_genome
Public archive
research-project
Python
•
MIT License
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
MicrobeMeter
Public
shiny-apps
R
•
MIT License
•0•0•0•0•Updated Aug 10, 2022Aug 10, 2022
alphafold_sm
Public
snakemake-pipelines alphafold2
Python
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MIT License
•0•0•0•0•Updated Aug 9, 2022Aug 9, 2022
MGSIM
Public
simulations genomes metagenomes
Python
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MIT License
•0•0•0•0•Updated Aug 9, 2022Aug 9, 2022
traitar3
Public
machine-learning bacteria phenotypes genomes archaea
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Aug 9, 2022Aug 9, 2022
gtdb_to_taxdump
Public
taxonomy databases gtdb
Python
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MIT License
•0•0•0•0•Updated Aug 9, 2022Aug 9, 2022
codiversification
Public
Code and notes for the Ley Lab's codiversification paper.
research-project
Jupyter Notebook
•1•4•0•0•Updated Aug 1, 2022Aug 1, 2022
TUK_db_shiny
Public
Shiny db viewer for TUK data
shiny-apps
R
•0•0•0•0•Updated Feb 10, 2022Feb 10, 2022
plateReaderShiny
Public
Shiny apps for interfacing with the lab plate readers
shiny-apps
R
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MIT License
•0•0•0•0•Updated Feb 10, 2022Feb 10, 2022