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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 102 33

  2. humann humann Public

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

    Python 172 58

  3. MetaPhlAn MetaPhlAn Public

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

    Python 301 86

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 127 33

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 118 35

  6. kneaddata kneaddata Public

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

    Python 107 28

Repositories

Showing 10 of 123 repositories
  • conda-biobakery Public

    A collection of conda build recipes

    biobakery/conda-biobakery’s past year of commit activity
    Shell 1 1 0 0 Updated Oct 29, 2024
  • maaslin3_lite Public

    Lefse like wrapper for MaAsLin3

    biobakery/maaslin3_lite’s past year of commit activity
    R 0 0 0 0 Updated Oct 28, 2024
  • 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 0 Apache-2.0 19 0 1 Updated Oct 24, 2024
  • phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    biobakery/phylophlan’s past year of commit activity
    Python 127 MIT 33 47 (2 issues need help) 1 Updated Oct 22, 2024
  • 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 301 MIT 86 0 4 Updated Oct 22, 2024
  • manuscript_parathaa Public

    Workflow to generate results for Parathaa manuscript

    biobakery/manuscript_parathaa’s past year of commit activity
    R 0 0 0 0 Updated Oct 21, 2024
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 10 0 0 0 Updated Oct 19, 2024
  • biobakery Public

    bioBakery tools for meta'omic profiling

    biobakery/biobakery’s past year of commit activity
    Shell 259 73 38 1 Updated Oct 19, 2024
  • omnibus-and-maaslin2-rscripts-and-hmp2-data Public

    Omnibus and Maaslin2 Rscripts and hmp2-data

    biobakery/omnibus-and-maaslin2-rscripts-and-hmp2-data’s past year of commit activity
    R 2 5 0 0 Updated Oct 19, 2024
  • metawibele Public

    MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

    biobakery/metawibele’s past year of commit activity
    Python 20 3 1 0 Updated Oct 17, 2024