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bioBakery

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129 repositories

fugassem
Public
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
python tools pubsub biobakery
Python
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Other
•0•20•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 bowtie2 biobakery kneaddata
Python
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Other
•34•140•0•0•Updated Dec 17, 2025Dec 17, 2025
Maaslin2
Public
MaAsLin2: Microbiome Multivariate Association with Linear Models
tools public metagenomics bioconductor repeated-measures microbiome false-discovery-rate biobakery differential-abundance-analysis multiple-covariates
R
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Other
•34•151•0•1•Updated Dec 16, 2025Dec 16, 2025
MetaPhlAn
Public
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
python tools public metagenomics biobakery
Python
•
MIT License
•91•387•0•1•Updated Dec 13, 2025Dec 13, 2025
baqlava
Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
Python
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Other
•0•7•0•0•Updated Dec 3, 2025Dec 3, 2025
humann
Public
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
python tools public biobakery
Python
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Other
•68•229•1•9•Updated Dec 1, 2025Dec 1, 2025
metawibele
Public
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
python tools public archived biobakery
Python
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Other
•3•23•1•0•Updated Nov 25, 2025Nov 25, 2025
maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
R
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Other
•9•51•0•1•Updated Nov 17, 2025Nov 17, 2025
portal-ui
Public
BIOM-Mass Data Portal UI (developed from the NCI-GDC portal UI framework)
web-contents biobakery
JavaScript
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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
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.
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)
R
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Other
•1•3•0•0•Updated Oct 20, 2025Oct 20, 2025
biobakery_workflows
Public
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
private analysis-workflows biobakery
Python
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Other
•39•130•5•2•Updated Oct 20, 2025Oct 20, 2025
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 efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).
python tools public biobakery
Python
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Other
•3•12•0•1•Updated Sep 8, 2025Sep 8, 2025
manuscript_parathaa
Public
Workflow to generate results for Parathaa manuscript
R
•0•1•0•0•Updated Aug 12, 2025Aug 12, 2025
conda-biobakery
Public
A collection of conda build recipes
public biobakery
Shell
•1•2•0•0•Updated Jul 28, 2025Jul 28, 2025
anpan
Public
R
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Other
•1•10•1•0•Updated Jul 21, 2025Jul 21, 2025
Macarron
Public
R
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Other
•0•4•0•0•Updated Jun 20, 2025Jun 20, 2025
phylophlan
Public
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools phylogenetic-trees biobakery
Python
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MIT License
•36•159•50•1•Updated Jun 16, 2025Jun 16, 2025
biobakery
Public
bioBakery tools for meta'omic profiling
devops tools biobakery
HTML
•79•299•39•1•Updated Jun 3, 2025Jun 3, 2025
MASLD
Public
R
•0•2•0•0•Updated Apr 21, 2025Apr 21, 2025
maaslin3_lite
Public
Lefse like wrapper for MaAsLin3
ReScript
•0•1•0•0•Updated Mar 25, 2025Mar 25, 2025
maaslin3_tutorial_files
Public
Outputs files for the MaAsLin 3 tutorial
Other
•0•1•0•0•Updated Mar 5, 2025Mar 5, 2025
teddy_genetics
Public
R
•0•0•0•0•Updated Feb 14, 2025Feb 14, 2025
galaxy_maaslin3
Public
Galaxy maaslin3 Main Program repository
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 metagenomic data and determine the presence and abundance of the protein families of interest.
python public biobakery
Python
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Other
•7•31•4•1•Updated Jan 24, 2025Jan 24, 2025
waafle
Public
http://huttenhower.sph.harvard.edu/waafle
Python
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Other
•1•22•0•0•Updated Dec 16, 2024Dec 16, 2024
SparseDOSSA2
Public
tools public bioconductor biobakery
HTML
•2•13•4•1•Updated Dec 2, 2024Dec 2, 2024
galaxy-upgrade
Public
Python
•0•1•3•0•Updated Nov 19, 2024Nov 19, 2024
firecloud-graphql
Public
GraphQL server and utilities scripts for the BIOM-Mass portal
misc biobakery
Python
•1•1•0•2•Updated Nov 16, 2024Nov 16, 2024