bioBakery

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126 repositories

maaslin3_lite
Public
Lefse like wrapper for MaAsLin3
Python
•0•1•0•0•Updated Feb 7, 2025Feb 7, 2025
galaxy_maaslin3
Public
Galaxy maaslin3 Main Program repository
0•0•0•0•Updated Feb 7, 2025Feb 7, 2025
kneaddata
Public
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
quality-control tools public biobakery bowtie2 kneaddata
Python
•
Other
•29•114•1•10•Updated Feb 6, 2025Feb 6, 2025
conda-biobakery
Public
A collection of conda build recipes
public biobakery
Shell
•1•2•0•0•Updated Feb 6, 2025Feb 6, 2025
baqlava
Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
Python
•
Other
•0•2•0•0•Updated Feb 4, 2025Feb 4, 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
•86•324•0•4•Updated Feb 4, 2025Feb 4, 2025
maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
R
•
Other
•1•25•0•0•Updated Jan 31, 2025Jan 31, 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
•5•28•4•1•Updated Jan 24, 2025Jan 24, 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
•34•106•5•2•Updated Jan 24, 2025Jan 24, 2025
anpan
Public
R
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Other
•1•8•1•0•Updated Jan 2, 2025Jan 2, 2025
phylophlan
Public
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools phylogenetic-trees biobakery
Python
•
MIT License
•33•133•47•1•Updated Dec 20, 2024Dec 20, 2024
teddy_genetics
Public
R
•0•0•0•0•Updated Dec 18, 2024Dec 18, 2024
waafle
Public
http://huttenhower.sph.harvard.edu/waafle
Python
•
Other
•1•11•0•0•Updated Dec 16, 2024Dec 16, 2024
fugassem
Public
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
python tools pubsub biobakery
Python
•
Other
•0•3•1•0•Updated Dec 3, 2024Dec 3, 2024
SparseDOSSA2
Public
tools public bioconductor biobakery
HTML
•2•13•4•1•Updated Dec 2, 2024Dec 2, 2024
maaslin3_tutorial_files
Public
Outputs files for the MaAsLin 3 tutorial
Other
•0•1•0•0•Updated Nov 24, 2024Nov 24, 2024
galaxy-upgrade
Public
Python
•0•1•2•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
Maaslin2
Public
MaAsLin2: Microbiome Multivariate Association with Linear Models
tools public metagenomics repeated-measures microbiome false-discovery-rate biobakery differential-abundance-analysis multiple-covariates bioconductor
R
•
Other
•35•131•0•1•Updated Nov 11, 2024Nov 11, 2024
portal-ui
Public
BIOM-Mass Data Portal UI (developed from the NCI-GDC portal UI framework)
web-contents biobakery
JavaScript
•
Apache License 2.0
•19•1•0•1•Updated Nov 1, 2024Nov 1, 2024
manuscript_parathaa
Public
Workflow to generate results for Parathaa manuscript
R
•0•1•0•0•Updated Oct 21, 2024Oct 21, 2024
biobakery
Public
bioBakery tools for meta'omic profiling
devops tools biobakery
Shell
•75•268•38•1•Updated Oct 19, 2024Oct 19, 2024
omnibus-and-maaslin2-rscripts-and-hmp2-data
Public
Omnibus and Maaslin2 Rscripts and hmp2-data
tools public archive biobakery
R
•5•3•0•0•Updated Oct 19, 2024Oct 19, 2024
metawibele
Public
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
python tools public archived biobakery
Python
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Other
•3•21•1•0•Updated Oct 17, 2024Oct 17, 2024
parathaa
Public
Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)
R
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Other
•0•3•0•0•Updated Sep 28, 2024Sep 28, 2024
pets_pooled_analysis
Public
R
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Other
•0•0•0•0•Updated Sep 19, 2024Sep 19, 2024
humann
Public
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
python tools public biobakery
Python
•
Other
•58•183•3•8•Updated Aug 16, 2024Aug 16, 2024
graphlan
Public
High-quality circular representations of taxonomic and phylogenetic trees
python tools phylogenetic-trees biobakery taxonomic-trees circular-visualization
Python
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MIT License
•28•92•1•2•Updated Aug 7, 2024Aug 7, 2024
halla
Public
Python
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Other
•3•12•0•0•Updated Jul 22, 2024Jul 22, 2024
MTX_model
Public
R package for differential expression analysis in metatranscriptomics
R
•
Other
•6•10•0•0•Updated Jul 18, 2024Jul 18, 2024