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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 123 38

  2. humann humann Public

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

    Python 218 66

  3. MetaPhlAn MetaPhlAn Public

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

    Python 375 91

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 158 34

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 148 34

  6. kneaddata kneaddata Public

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

    Python 133 33

Repositories

Showing 10 of 127 repositories
  • 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 375 MIT 91 0 1 Updated Oct 28, 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 15 0 2 0 Updated Oct 25, 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 Oct 25, 2025
  • parathaa Public

    Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)

    biobakery/parathaa’s past year of commit activity
    R 3 1 0 0 Updated Oct 20, 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 218 66 1 9 Updated Oct 20, 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 133 33 0 0 Updated Oct 20, 2025
  • biobakery_workflows Public

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

    biobakery/biobakery_workflows’s past year of commit activity
    Python 123 38 5 2 Updated Oct 20, 2025
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 47 8 0 2 Updated Oct 12, 2025
  • 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).

    biobakery/anadama2’s past year of commit activity
    Python 12 3 0 1 Updated Sep 8, 2025
  • manuscript_parathaa Public

    Workflow to generate results for Parathaa manuscript

    biobakery/manuscript_parathaa’s past year of commit activity
    R 1 0 0 0 Updated Aug 12, 2025
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