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@bailey-lab

Bailey Lab

Studying the genetics and genomics of infectious disease and immunity

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  1. MIPTools MIPTools Public

    A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

    Jupyter Notebook 7 9

  2. miplicorn miplicorn Public

    A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.

    R 3 2

  3. SeekDeep SeekDeep Public

    Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab

    C++ 16 6

  4. MIPWrangler MIPWrangler Public

    Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results

    C++ 1 1

  5. coiaf coiaf Public

    Complexity of Infection Estimation with Allele Frequencies

    R 3 2

  6. coiaf-real-data coiaf-real-data Public

    MalariaGEN Plasmodium falciparum Community Project analysis using coiaf

    HTML 6 1

Repositories

Showing 10 of 49 repositories
  • MIPTools Public

    A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

    bailey-lab/MIPTools’s past year of commit activity
    Jupyter Notebook 7 MIT 9 12 4 Updated Feb 25, 2025
  • SeekDeep Public

    Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab

    bailey-lab/SeekDeep’s past year of commit activity
    C++ 16 LGPL-3.0 6 9 0 Updated Feb 22, 2025
  • EBV-SWGA Public
    bailey-lab/EBV-SWGA’s past year of commit activity
    Python 0 0 0 0 Updated Feb 18, 2025
  • haplotype_variant_calling Public

    uses Nick Hathaway's variantCallOnSeqAndProtein script to call variants on vcf files and generate prevalences and amino acid calls

    bailey-lab/haplotype_variant_calling’s past year of commit activity
    Python 0 0 0 0 Updated Feb 5, 2025
  • seekdeep_prevalences Public

    converts amino acid counts files into miptools formatted counts that are suitable for prevalence estimates

    bailey-lab/seekdeep_prevalences’s past year of commit activity
    Python 0 0 0 0 Updated Jan 28, 2025
  • seekdeep_illumina_snakemake Public

    a basic workflow for running seekdeep pipelines in snakemake

    bailey-lab/seekdeep_illumina_snakemake’s past year of commit activity
    Python 1 0 1 0 Updated Jan 23, 2025
  • snakemake_R_maps Public

    a snakemake repo for mapping regional mutations in R

    bailey-lab/snakemake_R_maps’s past year of commit activity
    R 0 0 0 0 Updated Dec 3, 2024
  • labman_scripts Public

    growing set of utility scrips supporting lab work in the bailey lab

    bailey-lab/labman_scripts’s past year of commit activity
    Python 0 0 0 0 Updated Nov 20, 2024
  • MIPWrangler Public

    Bioinformatics tools to analyze molecular inversion probe (MIP) sequencing results

    bailey-lab/MIPWrangler’s past year of commit activity
    C++ 1 GPL-3.0 1 0 0 Updated Nov 12, 2024
  • miplicorn Public

    A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.

    bailey-lab/miplicorn’s past year of commit activity
    R 3 2 5 2 Updated Nov 4, 2024

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