biobakery repositories

134 repositories

maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
r-tools
r-tools
R
•
Other
•13•86•0•2•Updated Sep 12, 2026Sep 12, 2026
MetaPhlAn
Public
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
python tools public
python tools public metagenomics python-tools biobakery
Python
•
MIT License
•96•422•0•1•Updated Sep 10, 2026Sep 10, 2026
humann
Public
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
python tools public
python tools public python-tools biobakery
Python
•
Other
•74•252•1•14•Updated Sep 2, 2026Sep 2, 2026
HVP-nextflow
Public
HVP-nextflow pipeline
Python
•5•0•0•0•Updated Sep 2, 2026Sep 2, 2026
biobakery-nextflow
Public
Nextflow
•5•4•8•2•Updated Sep 2, 2026Sep 2, 2026
loCHO_microbiome
Public
Repository that contains code used to analysis feature tables in association with the loCHO microbiome publication.
analyses biobakery
analyses biobakery
R
•0•0•0•0•Updated Aug 12, 2026Aug 12, 2026
biobakery_workflows
Public
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.…
python-tools biobakery
python-tools biobakery
Python
•
Other
•41•140•5•2•Updated Aug 6, 2026Aug 6, 2026
anpan
Public
Modeling strain-level variation by gene, phylogeny, or pathway
r-tools
r-tools
R
•
Other
•1•14•1•0•Updated Aug 6, 2026Aug 6, 2026
biobakery
Public
bioBakery tools for meta'omic profiling
documentation devops tools
documentation devops tools biobakery
HTML
•
Other
•82•324•39•1•Updated Aug 4, 2026Aug 4, 2026
cpn60
Public
Using the housekeeping gene cpn60 as a marker for microbial community profiling and viability assessment
analyses biobakery
analyses biobakery
R
•0•0•0•0•Updated Aug 3, 2026Aug 3, 2026
conda-biobakery
Public
A collection of conda build recipes
public biobakery
public biobakery
Shell
•1•2•0•0•Updated Jul 31, 2026Jul 31, 2026
permaBrioche
Public
PERMANOVA with Block/Repeat-measures Including Observational Causal Hajek Estimator
R
•
Other
•0•0•0•0•Updated Jul 30, 2026Jul 30, 2026
baqlava
Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
python-tools
python-tools
Python
•
Other
•3•18•0•0•Updated Jul 13, 2026Jul 13, 2026
kneaddata
Public
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
quality-control tools public
quality-control tools public bowtie2 python-tools biobakery kneaddata
Python
•
Other
•37•155•0•0•Updated Jul 11, 2026Jul 11, 2026
teddy_genetics
Public
analyses
analyses
R
•0•0•0•0•Updated Jul 4, 2026Jul 4, 2026
waafle
Public
http://huttenhower.sph.harvard.edu/waafle
python-tools
python-tools
Python
•
Other
•2•24•0•0•Updated Jun 16, 2026Jun 16, 2026
phylophlan
Public
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools phylogenetic-trees
python tools phylogenetic-trees python-tools biobakery
Python
•
MIT License
•36•170•48•1•Updated Jun 10, 2026Jun 10, 2026
baqlava-analysis
Public
analyses
analyses
Jupyter Notebook
•0•0•0•0•Updated Jun 1, 2026Jun 1, 2026
Macarron
Public
r-tools
r-tools
R
•
Other
•0•4•0•0•Updated Apr 8, 2026Apr 8, 2026
anadama2
Public
AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it e…
python tools public
python tools public python-tools biobakery
Python
•
Other
•3•12•0•1•Updated Mar 25, 2026Mar 25, 2026
maaslin3_benchmark
Public
Benchmarking for MaAsLin 3
analyses
analyses
R
•
MIT License
•0•0•0•0•Updated Feb 23, 2026Feb 23, 2026
Maaslin2
Public
MaAsLin2: Microbiome Multivariate Association with Linear Models
tools public metagenomics
tools public metagenomics bioconductor repeated-measures microbiome false-discovery-rate biobakery differential-abundance-analysis multiple-covariates
R
•
Other
•35•154•0•1•Updated Feb 5, 2026Feb 5, 2026
MMUPHin
Public
MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
tools public bioconductor
tools public bioconductor biobakery r-tools
R
•
Other
•4•12•1•0•Updated Jan 31, 2026Jan 31, 2026
fugassem
Public
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
python tools pubsub
python tools pubsub python-tools biobakery
Python
•
Other
•2•21•2•0•Updated Dec 26, 2025Dec 26, 2025
metawibele
Public
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
python tools public
python tools public python-tools biobakery
Python
•
Other
•3•23•1•0•Updated Nov 25, 2025Nov 25, 2025
portal-ui
Public
BIOM-Mass Data Portal UI (developed from the NCI-GDC portal UI framework)
web-contents biobakery
web-contents biobakery
JavaScript
•
Apache License 2.0
•19•1•0•1•Updated Oct 31, 2025Oct 31, 2025
parathaa
Public
Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)
python-tools
python-tools
R
•
Other
•2•3•0•0•Updated Oct 20, 2025Oct 20, 2025
manuscript_parathaa
Public
Workflow to generate results for Parathaa manuscript
analyses
analyses
R
•0•1•0•0•Updated Aug 12, 2025Aug 12, 2025
MASLD
Public
analyses
analyses
R
•0•2•0•0•Updated Apr 21, 2025Apr 21, 2025
maaslin3_lite
Public
Lefse like wrapper for MaAsLin3
r-tools
r-tools
ReScript
•0•1•0•0•Updated Mar 25, 2025Mar 25, 2025

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bioBakery

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134 repositories

maaslin3

MetaPhlAn

humann

HVP-nextflow

biobakery-nextflow

loCHO_microbiome

biobakery_workflows

anpan

biobakery

cpn60

conda-biobakery

permaBrioche

baqlava

kneaddata

teddy_genetics

waafle

phylophlan

baqlava-analysis

Macarron

anadama2

maaslin3_benchmark

Maaslin2

MMUPHin

fugassem

metawibele

portal-ui

parathaa

manuscript_parathaa

MASLD

maaslin3_lite

Repositories list

134 repositories