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gentb-site
gentb-site PublicThe genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
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mtb-illumina-wgs-evaluation
mtb-illumina-wgs-evaluation PublicRepository for analysis of Benchmarking the accuracy of short-read sequencing across the M. tuberculosis genome, 2022, Bioinformatics.
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Repositories
- 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)
- gentb-site Public
The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
- tbp-severity-scoring Public
- JM_espA_modeling Public
This repository contains the codes of Jiazheng Miao's (MBI Class of 2025) Capstone Project, a mathematical modeling on the expression level of espA in Mycobacterium tuberculosis.
- gentb-snakemake Public
From FASTQ file to antibiotic resistance prediction using RandomForest - the GenTB pipeline wrapped in snakemake
- DependentMutations Public
- 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)
- 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)
- 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)
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