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@biobakery

bioBakery

Software, documentation, and tutorials for microbial community profiling.

Pinned

  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 96 33

  2. humann humann Public

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

    Python 161 56

  3. MetaPhlAn MetaPhlAn Public

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

    Python 287 83

  4. phylophlan phylophlan Public

    Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

    Python 120 33

  5. Maaslin2 Maaslin2 Public

    MaAsLin2: Microbiome Multivariate Association with Linear Models

    R 112 35

  6. kneaddata kneaddata Public

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

    Python 103 27

Repositories

Showing 10 of 122 repositories
  • maaslin3 Public

    MaAsLin3: Microbiome Multivariate Association with Linear Models

    biobakery/maaslin3’s past year of commit activity
    R 4 0 0 0 Updated Aug 24, 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 287 MIT 83 0 5 Updated Aug 23, 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 Aug 19, 2024
  • pets_pooled_analysis Public
    biobakery/pets_pooled_analysis’s past year of commit activity
    R 0 0 0 0 Updated Aug 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 Aug 16, 2024
  • 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 161 56 3 8 Updated Aug 16, 2024
  • anpan Public
    biobakery/anpan’s past year of commit activity
    R 6 0 0 0 Updated Aug 13, 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 0 Updated Aug 12, 2024
  • 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 2 0 1 0 Updated Aug 12, 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 Aug 8, 2024
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