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MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing databiobakery
bioBakery tools for meta'omic profilinghumann
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomesMaaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Modelskneaddata
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.biobakery_workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.graphlan
High-quality circular representations of taxonomic and phylogenetic treesMetaPhlAn2
shortbred
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.metawibele
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiomeSparseDOSSA2
halla
homebrew-biobakery
Biobakery formulae for the Homebrew package manageranadama2
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).MTX_model
R package for differential expression analysis in metatranscriptomicsbanocc
MMUPHin
MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studiesmaaslin
MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.anpan
sparseDOSSA
ccrepe
The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.ibd_paper
hmp2_analysis
meddiet2020
micropita
cgfp
uniref_annotator
waafle
http://huttenhower.sph.harvard.edu/waafleMacarron
omnibus-and-maaslin2-rscripts-and-hmp2-data
Omnibus and Maaslin2 Rscripts and hmp2-datahumann_legacy
maaslin2_benchmark
Large-scale Benchmarking of Microbial Multivariable Association Methodsbreadcrumbs
galaxy_lefse
crc-subtyping-paper
parathaa
Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)fugassem
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomeshalla_legacy
Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.MTX_synthetic
Synthetic data generation for the mtx2021 projectjdrf2
pouchitis
synmetap
galaxy-upgrade
ibd_meta_analysis
sparsedossa_paper
conda-biobakery
A collection of conda build recipesqiimetomaaslin
ppanini
Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network IntegrationPhysical-activity-gut-microbiome-body-weight
maaslin3
MaAsLin3: Microbiome Multivariate Association with Linear ModelsLove Open Source and this site? Check out how you can help us