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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 94 33

  2. humann humann Public

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

    Python 152 56

  3. MetaPhlAn MetaPhlAn Public

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

    Python 282 78

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 118 32

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 110 35

  6. kneaddata kneaddata Public

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

    Python 101 27

Repositories

Showing 10 of 120 repositories
  • graphlan Public

    High-quality circular representations of taxonomic and phylogenetic trees

    biobakery/graphlan’s past year of commit activity
    Python 84 MIT 28 1 3 Updated Jul 19, 2024
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 1 0 0 0 Updated Jul 19, 2024
  • maaslin3_lite Public

    Lefse like wrapper for MaAsLin3

    biobakery/maaslin3_lite’s past year of commit activity
    R 0 0 0 0 Updated Jul 19, 2024
  • MTX_model Public

    R package for differential expression analysis in metatranscriptomics

    biobakery/MTX_model’s past year of commit activity
    R 8 5 0 0 Updated Jul 18, 2024
  • conda-biobakery Public

    A collection of conda build recipes

    biobakery/conda-biobakery’s past year of commit activity
    Shell 1 1 0 0 Updated Jul 17, 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 282 MIT 78 0 2 Updated Jul 16, 2024
  • biobakery Public

    bioBakery tools for meta'omic profiling

    biobakery/biobakery’s past year of commit activity
    Shell 253 72 38 1 Updated Jul 15, 2024
  • Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    biobakery/Maaslin2’s past year of commit activity
    R 110 35 0 1 Updated Jul 15, 2024
  • parathaa Public

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

    biobakery/parathaa’s past year of commit activity
    R 2 0 0 1 Updated Jul 10, 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 Jul 9, 2024
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