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@biobakery

bioBakery

Software, documentation, and tutorials for microbial community profiling.

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  1. biobakery_workflows biobakery_workflows Public

    bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

    Python 130 39

  2. humann humann Public

    HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

    Python 232 68

  3. MetaPhlAn MetaPhlAn Public

    MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

    Python 391 91

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 159 36

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 152 35

  6. kneaddata kneaddata Public

    Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

    Python 142 34

Repositories

Showing 10 of 129 repositories
  • humann Public

    HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

    biobakery/humann’s past year of commit activity
    Python 232 68 1 8 Updated Jan 20, 2026
  • MMUPHin Public

    MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

    biobakery/MMUPHin’s past year of commit activity
    R 9 4 1 0 Updated Jan 16, 2026
  • teddy_genetics Public
    biobakery/teddy_genetics’s past year of commit activity
    R 0 0 0 0 Updated Jan 16, 2026
  • fugassem Public

    FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes

    biobakery/fugassem’s past year of commit activity
    Python 20 0 2 0 Updated Dec 26, 2025
  • kneaddata Public

    Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

    biobakery/kneaddata’s past year of commit activity
    Python 142 34 0 0 Updated Dec 17, 2025
  • Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    biobakery/Maaslin2’s past year of commit activity
    R 152 35 0 1 Updated Dec 16, 2025
  • MetaPhlAn Public

    MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

    biobakery/MetaPhlAn’s past year of commit activity
    Python 391 MIT 91 0 1 Updated Dec 13, 2025
  • baqlava Public

    Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy

    biobakery/baqlava’s past year of commit activity
    Python 7 0 0 0 Updated Dec 3, 2025
  • metawibele Public

    MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

    biobakery/metawibele’s past year of commit activity
    Python 23 3 1 0 Updated Nov 25, 2025
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 64 11 0 4 Updated Nov 17, 2025
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