bioBakery

All

125 repositories

maaslin3_lite
Public
Lefse like wrapper for MaAsLin3
Python
•0•1•0•0•Updated Jan 19, 2025Jan 19, 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•319•0•4•Updated Jan 17, 2025Jan 17, 2025
maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
R
•
Other
•1•23•0•0•Updated Jan 13, 2025Jan 13, 2025
baqlava
Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
Python
•
Other
•0•2•0•0•Updated Jan 10, 2025Jan 10, 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•113•1•11•Updated Jan 6, 2025Jan 6, 2025
anpan
Public
R
•
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•132•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•10•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
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
•
Other
•34•106•5•2•Updated Nov 16, 2024Nov 16, 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•130•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
conda-biobakery
Public
A collection of conda build recipes
public biobakery
Shell
•1•2•0•0•Updated Oct 29, 2024Oct 29, 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•265•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
•
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
•
Other
•0•3•0•0•Updated Sep 28, 2024Sep 28, 2024
pets_pooled_analysis
Public
R
•
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•181•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
•
MIT License
•28•92•1•2•Updated Aug 7, 2024Aug 7, 2024
halla
Public
Python
•
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
MASLD
Public
R
•0•0•0•0•Updated Jul 5, 2024Jul 5, 2024
Macarron
Public
R
•
Other
•0•3•0•0•Updated Jun 25, 2024Jun 25, 2024