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130 repositories

maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
r-tools
r-tools
R
•
Other
•12•82•0•2•Updated Apr 24, 2026Apr 24, 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
•39•132•5•2•Updated Apr 22, 2026Apr 22, 2026
baqlava
Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
python-tools
python-tools
Python
•
Other
•2•14•0•0•Updated Apr 12, 2026Apr 12, 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
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
•91•401•0•1•Updated Mar 16, 2026Mar 16, 2026
waafle
Public
http://huttenhower.sph.harvard.edu/waafle
python-tools
python-tools
Python
•
Other
•2•24•0•0•Updated Feb 26, 2026Feb 26, 2026
maaslin3_benchmark
Public
Benchmarking for MaAsLin 3
analyses
analyses
R
•
MIT License
•0•0•0•0•Updated Feb 23, 2026Feb 23, 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•164•48•1•Updated Feb 13, 2026Feb 13, 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•9•1•0•Updated Jan 31, 2026Jan 31, 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
•70•242•1•8•Updated Jan 20, 2026Jan 20, 2026
teddy_genetics
Public
analyses
analyses
R
•0•0•0•0•Updated Jan 16, 2026Jan 16, 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
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
•35•146•0•0•Updated Dec 17, 2025Dec 17, 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
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 Oct 30, 2025Oct 30, 2025
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 Oct 22, 2025Oct 22, 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
conda-biobakery
Public
A collection of conda build recipes
public biobakery
public biobakery
Shell
•1•2•0•0•Updated Jul 28, 2025Jul 28, 2025
anpan
Public
r-tools
r-tools
R
•
Other
•1•13•1•0•Updated Jul 21, 2025Jul 21, 2025
biobakery
Public
bioBakery tools for meta'omic profiling
documentation devops tools
documentation devops tools biobakery
HTML
•81•313•39•1•Updated Jun 3, 2025Jun 3, 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
maaslin3_tutorial_files
Public
Outputs files for the MaAsLin 3 tutorial
analyses
analyses
Other
•0•1•0•0•Updated Mar 5, 2025Mar 5, 2025
galaxy_maaslin3
Public
Galaxy maaslin3 Main Program repository
galaxy
galaxy
0•0•0•0•Updated Feb 7, 2025Feb 7, 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 public python-tools
python public python-tools biobakery
Python
•
Other
•7•31•4•1•Updated Jan 24, 2025Jan 24, 2025
SparseDOSSA2
Public
tools public bioconductor
tools public bioconductor biobakery r-tools
HTML
•2•13•4•1•Updated Dec 2, 2024Dec 2, 2024

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bioBakery

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130 repositories

maaslin3

biobakery_workflows

baqlava

Macarron

anadama2

MetaPhlAn

waafle

maaslin3_benchmark

phylophlan

Maaslin2

MMUPHin

humann

teddy_genetics

fugassem

kneaddata

metawibele

portal-ui

cpn60

loCHO_microbiome

parathaa

manuscript_parathaa

conda-biobakery

anpan

biobakery

MASLD

maaslin3_lite

maaslin3_tutorial_files

galaxy_maaslin3

shortbred

SparseDOSSA2

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Repositories list

130 repositories