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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 9 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 5 2

  3. SeekDeep SeekDeep Public

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

    C++ 18 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 4 2

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

    MalariaGEN Plasmodium falciparum Community Project analysis using coiaf

    HTML 6 1

Repositories

Showing 10 of 50 repositories
  • 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 5 2 5 2 Updated Jul 27, 2026
  • 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++ 18 LGPL-3.0 6 9 0 Updated Jul 23, 2026
  • 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 9 MIT 9 12 3 Updated May 26, 2026
  • coatswga Public

    Coverage Optimizing and Accurate Toolkit for selective whole genome amplification (sWGA)

    bailey-lab/coatswga's past year of commit activity
    Python 3 GPL-3.0 0 1 0 Updated Apr 20, 2026
  • 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 Apr 1, 2026
  • compilerProfiler Public

    C++ library with an aligner to test different compiler speeds with different optimizations

    bailey-lab/compilerProfiler's past year of commit activity
    C++ 0 GPL-2.0 1 0 0 Updated Apr 1, 2026
  • bailey-lab/Po_popgen_snakemake's past year of commit activity
    Python 0 0 0 0 Updated Mar 20, 2026
  • msmt_dr_longitudinal_21-23 Public

    repo for a manuscript describing msmt longitudinal data from 2021-2023

    bailey-lab/msmt_dr_longitudinal_21-23's past year of commit activity
    HTML 0 0 0 0 Updated Mar 6, 2026
  • count_undetermined_sample_barcodes Public

    when demultiplexing fails, we need the ability to figure out which sample barcodes were present and in what abundances. This allows us to figure out if the 'wrong' barcodes were applied to the samples or if the barcoding failed.

    bailey-lab/count_undetermined_sample_barcodes's past year of commit activity
    Python 0 0 0 0 Updated Oct 10, 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 Aug 18, 2025