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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 106 34

  2. humann humann Public

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

    Python 184 60

  3. MetaPhlAn MetaPhlAn Public

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

    Python 323 87

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 133 33

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 131 35

  6. kneaddata kneaddata Public

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

    Python 114 30

Repositories

Showing 10 of 126 repositories
  • teddy_genetics Public
    biobakery/teddy_genetics’s past year of commit activity
    R 0 0 0 0 Updated Feb 14, 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 3 0 1 0 Updated Feb 14, 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 114 30 1 11 Updated Feb 13, 2025
  • baqlava Public

    Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy

    biobakery/baqlava’s past year of commit activity
    Python 3 0 0 0 Updated Feb 13, 2025
  • maaslin3_lite Public

    Lefse like wrapper for MaAsLin3

    biobakery/maaslin3_lite’s past year of commit activity
    Python 1 0 0 0 Updated Feb 7, 2025
  • galaxy_maaslin3 Public

    Galaxy maaslin3 Main Program repository

    biobakery/galaxy_maaslin3’s past year of commit activity
    0 0 0 0 Updated Feb 7, 2025
  • conda-biobakery Public

    A collection of conda build recipes

    biobakery/conda-biobakery’s past year of commit activity
    Shell 2 1 0 0 Updated Feb 6, 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 323 MIT 87 0 4 Updated Feb 4, 2025
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 25 1 0 0 Updated Jan 31, 2025
  • shortbred Public

    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.

    biobakery/shortbred’s past year of commit activity
    Python 28 5 4 1 Updated Jan 24, 2025
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