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@bokulich-lab Laboratory of Food Systems Biotechnology

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    30 repositories

    • nf-ducken

      Public
      Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.
      Nextflow
      •2•3•44•0•Updated Oct 18, 2024Oct 18, 2024

    • RESCRIPt

      Public
      REference Sequence annotation and CuRatIon Pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •26•90•17•0•Updated Oct 17, 2024Oct 17, 2024

    • q2-amrfinderplus

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • q2-viromics

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • moshpit-docs

      Public
      MOSHPIT plugin suite documentation
      TeX
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • q2-amr

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•7•3•Updated Oct 4, 2024Oct 4, 2024

    • q2-assembly

      Public
      QIIME 2 plugin for (meta)genome assembly.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•4•8•1•Updated Oct 4, 2024Oct 4, 2024

    • q2-fondue

      Public
      Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•20•11•1•Updated Oct 4, 2024Oct 4, 2024

    • q2-moshpit

      Public
      MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•3•22•4•Updated Oct 3, 2024Oct 3, 2024

    • FermDB

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Sep 29, 2024Sep 29, 2024

    • uzh-microbiome-tutorial

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •2•3•0•0•Updated Sep 6, 2024Sep 6, 2024

    • q2-kmerizer

      Public
      QIIME 2 plugin for generating kmers from biological sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • mishmash

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•7•0•Updated Aug 23, 2024Aug 23, 2024

    • DataVisualizationBook

      Public
      JupyterBook on data visualization for Food Scientists.
      Jupyter Notebook
      •1•0•1•0•Updated Aug 14, 2024Aug 14, 2024

    • q2-virsorter2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•2•Updated Jul 18, 2024Jul 18, 2024

    • Fermented-Food-Ontologies

      Public
      Substrate-based fermented food ontologies
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•1•Updated Jul 12, 2024Jul 12, 2024

    • q2-pinocchio

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•1•Updated Jul 3, 2024Jul 3, 2024

    • fgcz-metagenomics-workshop

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • q2-checkm

      Public
      QIIME 2 plugin for assessing the quality of (meta)genomes using CheckM.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•2•0•Updated Jun 5, 2024Jun 5, 2024

    • utilities

      Public
      A collection of utilities used across repos.
      Shell
      •0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • q2-types-genomics

      Public archive
      QIIME 2 types for genomics plugins.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•6•5•0•Updated May 21, 2024May 21, 2024

    • q2-exonerate

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • advanced-comp-bio-tutorial

      Public
      Hands-on demonstration of 16S rRNA gene sequence analysis for SysBio Advanced Block Course 2022
      Jupyter Notebook
      •
      Apache License 2.0
      •2•4•1•0•Updated May 29, 2023May 29, 2023

    • q2-fondue-examples

      Public
      Materials accompanying q2-fondue article.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated Aug 31, 2022Aug 31, 2022

    • q2-protein-pca

      Public
      QIIME2 plugin for PCA analysis of protein sequence phylogeny.
      pcaqiime2protein
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•9•0•Updated Jul 12, 2022Jul 12, 2022

    • q2-plugin-template

      Public template
      A skeleton for QIIME 2 plugins
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•0•Updated Jun 29, 2022Jun 29, 2022

    • cancer-microbiome-intervention-tutorial

      Public
      JupyterBook for QIIME 2 FAES January 2022 workshop
      Jupyter Notebook
      •
      Other
      •15•0•0•0•Updated Jun 2, 2022Jun 2, 2022

    • HPV-multiOmics

      Public
      Multi-Omics Predictive Modelling of Cervicovaginal Microenvironment
      Python
      •2•3•0•0•Updated Feb 28, 2022Feb 28, 2022

    • q2-coordinates

      Public
      methods for geographic mapping of qiime2 artifact data or metadata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•2•10•0•Updated Feb 4, 2022Feb 4, 2022

    • db-benchmarks-2020

      Public
      Database benchmarks using RESCRIPt
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•0•0•Updated Oct 11, 2021Oct 11, 2021