bioBakery

All

123 repositories

maaslin3
Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
R
•
Other
•0•10•0•0•Updated Oct 30, 2024Oct 30, 2024
conda-biobakery
Public
A collection of conda build recipes
public biobakery
Shell
•1•1•0•0•Updated Oct 29, 2024Oct 29, 2024
maaslin3_lite
Public
Lefse like wrapper for MaAsLin3
R
•0•0•0•0•Updated Oct 28, 2024Oct 28, 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•0•0•1•Updated Oct 24, 2024Oct 24, 2024
phylophlan
Public
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools phylogenetic-trees biobakery
Python
•
MIT License
•33•127•47•1•Updated Oct 22, 2024Oct 22, 2024
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•301•0•4•Updated Oct 22, 2024Oct 22, 2024
manuscript_parathaa
Public
Workflow to generate results for Parathaa manuscript
R
•0•0•0•0•Updated Oct 21, 2024Oct 21, 2024
biobakery
Public
bioBakery tools for meta'omic profiling
devops tools biobakery
Shell
•73•259•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•2•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•20•1•0•Updated Oct 17, 2024Oct 17, 2024
waafle
Public
http://huttenhower.sph.harvard.edu/waafle
Python
•
Other
•1•4•0•0•Updated Oct 16, 2024Oct 16, 2024
firecloud-graphql
Public
GraphQL server and utilities scripts for the BIOM-Mass portal
misc biobakery
Python
•1•0•0•2•Updated Oct 15, 2024Oct 15, 2024
parathaa
Public
Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)
R
•
Other
•0•2•0•0•Updated Sep 28, 2024Sep 28, 2024
pets_pooled_analysis
Public
R
•
Other
•0•0•0•0•Updated Sep 19, 2024Sep 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
•33•102•5•2•Updated Sep 18, 2024Sep 18, 2024
humann
Public
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
python tools public biobakery
Python
•
Other
•58•172•3•8•Updated Aug 16, 2024Aug 16, 2024
anpan
Public
R
•
Other
•0•6•1•0•Updated Aug 13, 2024Aug 13, 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•2•1•0•Updated Aug 12, 2024Aug 12, 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•88•1•2•Updated Aug 7, 2024Aug 7, 2024
halla
Public
Python
•
Other
•3•12•0•0•Updated Jul 22, 2024Jul 22, 2024
maaslin3_tutorial_files
Public
Outputs files for the MaAsLin 3 tutorial
0•0•0•0•Updated Jul 22, 2024Jul 22, 2024
MTX_model
Public
R package for differential expression analysis in metatranscriptomics
R
•
Other
•6•9•0•0•Updated Jul 18, 2024Jul 18, 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•118•0•1•Updated Jul 15, 2024Jul 15, 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
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
•
Other
•3•12•0•1•Updated Jun 20, 2024Jun 20, 2024
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
•28•107•1•10•Updated Jun 4, 2024Jun 4, 2024
MMUPHin
Public
MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
tools public bioconductor biobakery
R
•
Other
•4•7•0•0•Updated May 19, 2024May 19, 2024
Analysis-workflows-template
Public template
Template repository for private analysis workflows
Python
•0•0•0•0•Updated May 15, 2024May 15, 2024
galaxy-upgrade
Public
Python
•0•0•2•0•Updated Apr 4, 2024Apr 4, 2024