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@Snitkin-Lab-Umich

Snitkin-Lab-Umich

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  1. prewas prewas Public

    R package to perform data pre-processing for more informative bacterial GWAS

    R 5 3

  2. hogwash hogwash Public

    Forked from katiesaund/hogwash

    Three bacterial GWAS methods all rolled into one easy-to-use R package

    R 1

  3. cognac cognac Public

    Forked from rdcrawford/cognac

    cognac: COre GeNe Alignment Concatenation

    C++ 1

  4. snitkitr snitkitr Public

    common R functions used in the lab

    R 1 1

  5. regentrans regentrans Public

    regentrans: R package for investigating regional pathogen transmission using genomic data

    R 5 1

  6. Comparative_Genomics Comparative_Genomics Public

    Forked from alipirani88/Comparative_Genomics

    Microbial Bioinformatics Workshop

    Shell 1 1

Repositories

Showing 10 of 33 repositories
  • funQCD Public

    Quality control pipeline for short read fungal data

    Snitkin-Lab-Umich/funQCD’s past year of commit activity
    Python 0 0 0 0 Updated Nov 21, 2024
  • snpkit-smk Public

    Snakemake workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.

    Snitkin-Lab-Umich/snpkit-smk’s past year of commit activity
    Python 0 0 5 0 Updated Nov 18, 2024
  • QCD Public

    Runs Quality Control workflow on Illumina WGS data

    Snitkin-Lab-Umich/QCD’s past year of commit activity
    Python 1 1 1 1 Updated Nov 18, 2024
  • Snitkin-Lab-Umich/Data-Flow-SOP’s past year of commit activity
    Python 0 0 0 0 Updated Nov 12, 2024
  • nanoQC Public

    Quality control pipeline for nanopore long read data

    Snitkin-Lab-Umich/nanoQC’s past year of commit activity
    Python 0 0 0 0 Updated Aug 27, 2024
  • Snitkin-Lab-Umich/Anaerobe-genomics-workshop’s past year of commit activity
    0 0 0 0 Updated Jul 6, 2024
  • Nanosake Public Forked from alipirani88/Nanosake

    A Snakemake workflow to basecall, quality control and assemble Nanopore data.

    Snitkin-Lab-Umich/Nanosake’s past year of commit activity
    Python 0 2 0 0 Updated May 28, 2024
  • snpkit Public Forked from alipirani88/snpkit

    A Modular/Scalable workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.

    Snitkin-Lab-Umich/snpkit’s past year of commit activity
    Python 2 MIT 5 0 0 Updated May 15, 2024
  • MICRO582-EPI582-Winter-2024 Public

    MICRO582/EPI582 - Genomic Epidemiology Winter Course 2022

    Snitkin-Lab-Umich/MICRO582-EPI582-Winter-2024’s past year of commit activity
    HTML 3 1 1 0 Updated Apr 3, 2024
  • eip-cre-transmission-ms Public

    Code and data related to EIP CRE transmission project

    Snitkin-Lab-Umich/eip-cre-transmission-ms’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Aug 3, 2023

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