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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 127 38

  2. humann humann Public

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

    Python 224 67

  3. MetaPhlAn MetaPhlAn Public

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

    Python 382 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 150 34

  6. kneaddata kneaddata Public

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

    Python 136 33

Repositories

Showing 10 of 129 repositories
  • 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
  • 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 224 67 1 8 Updated Dec 1, 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 382 MIT 91 0 1 Updated Nov 27, 2025
  • metawibele Public

    MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

    biobakery/metawibele’s past year of commit activity
    Python 22 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 49 8 0 1 Updated Nov 17, 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 136 33 0 0 Updated Nov 8, 2025
  • portal-ui Public Forked from IGS/portal-ui

    BIOM-Mass Data Portal UI (developed from the NCI-GDC portal UI framework)

    biobakery/portal-ui’s past year of commit activity
    JavaScript 1 Apache-2.0 19 0 1 Updated Oct 31, 2025
  • cpn60 Public

    Using the housekeeping gene cpn60 as a marker for microbial community profiling and viability assessment

    biobakery/cpn60’s past year of commit activity
    R 0 0 0 0 Updated Oct 30, 2025
  • 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 17 0 2 0 Updated Oct 25, 2025
  • loCHO_microbiome Public

    Repository that contains code used to analysis feature tables in association with the loCHO microbiome publication.

    biobakery/loCHO_microbiome’s past year of commit activity
    R 0 0 0 0 Updated Oct 22, 2025
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