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@farhat-lab

Farhat Laboratory

TB Genetics Bioinformatics

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  1. wdnn wdnn Public

    Wide and Deep Neural Net for predicting TB resistance from genotypic data

    Python 14 13

  2. fast-lineage-caller fast-lineage-caller Public

    Python 12 4

  3. gentb-site gentb-site Public

    The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens

    HTML 8 11

  4. resdata-ng resdata-ng Public

    DB of MTB resistance data and isolate metadata

    Python 6 1

  5. mtb-illumina-wgs-evaluation mtb-illumina-wgs-evaluation Public

    Repository for analysis of Benchmarking the accuracy of short-read sequencing across the M. tuberculosis genome, 2022, Bioinformatics.

    Jupyter Notebook 6

  6. fast-lineage-caller-vcf fast-lineage-caller-vcf Public

    Python 4 2

Repositories

Showing 10 of 28 repositories
  • who-analysis Public

    Code used for WHO analysis work

    farhat-lab/who-analysis’s past year of commit activity
    Jupyter Notebook 2 MIT 1 0 0 Updated Jul 18, 2024
  • mtb-pg-benchmarking-2024paper Public

    All code for data processing and analysis described in "Analysis of the limited M. tuberculosis pangenome reveals potential pitfalls of pan-genome analysis approaches" (Marin-2024)

    farhat-lab/mtb-pg-benchmarking-2024paper’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Apr 10, 2024
  • gentb-snakemake Public

    From FASTQ file to antibiotic resistance prediction using RandomForest - the GenTB pipeline wrapped in snakemake

    farhat-lab/gentb-snakemake’s past year of commit activity
    HTML 1 3 3 1 Updated Jun 29, 2023
  • DependentMutations Public
    farhat-lab/DependentMutations’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated Jun 5, 2023
  • phase-variation-in-Mtbc Public

    Jupyter Notebooks used in data analysis for "Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex" (Vargas et al. 2023)

    farhat-lab/phase-variation-in-Mtbc’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated May 30, 2023
  • in-host-Mtbc-dynamics Public

    Jupyter Notebooks used in data analysis for "In-host population dynamics of Mycobacterium tuberculosis complex during active disease" (Vargas et al. 2021)

    farhat-lab/in-host-Mtbc-dynamics’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated May 30, 2023
  • epistasis-KAN-BDQ-Mtbc-resistance Public

    Jupyter Notebooks used in data analysis for "The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in Mycobacterium tuberculosis complex" (Vargas et al. 2021)

    farhat-lab/epistasis-KAN-BDQ-Mtbc-resistance’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated May 29, 2023
  • gentb-site Public

    The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens

    farhat-lab/gentb-site’s past year of commit activity
    HTML 8 11 9 3 Updated Apr 16, 2023
  • mtb-illumina-wgs-evaluation Public

    Repository for analysis of Benchmarking the accuracy of short-read sequencing across the M. tuberculosis genome, 2022, Bioinformatics.

    farhat-lab/mtb-illumina-wgs-evaluation’s past year of commit activity
    Jupyter Notebook 6 MIT 0 0 1 Updated Aug 9, 2022
  • megapipe Public

    A wrapper pipe for variant calling and genome assembly for M.tuberculosis

    farhat-lab/megapipe’s past year of commit activity
    Python 3 1 2 0 Updated May 27, 2022
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