Repositories list

• 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)

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Jan 30, 2025Jan 30, 2025

• who-analysis

  Public
  Code used for WHO analysis work

  Jupyter Notebook

  •

  MIT License

  •1•2•0•0•Updated Jan 13, 2025Jan 13, 2025

• 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.

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• gentb-snakemake

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

  HTML

  •3•1•4•1•Updated Jun 29, 2023Jun 29, 2023

• DependentMutations

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Jun 5, 2023Jun 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)

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated May 30, 2023May 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)

  Jupyter Notebook

  •1•0•0•0•Updated May 30, 2023May 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)

  Jupyter Notebook

  •2•0•0•0•Updated May 29, 2023May 29, 2023

• gentb-site

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

  HTML

  •

  Other

  •11•8•9•3•Updated Apr 16, 2023Apr 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.

  Jupyter Notebook

  •

  MIT License

  •0•6•0•1•Updated Aug 9, 2022Aug 9, 2022

• megapipe

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

  Python

  •1•3•2•0•Updated May 27, 2022May 27, 2022

• AISC610_darwinian_medicine

  Public
  Practical exercises for the Darwinian Medicine class of the AISC610 course

  Jupyter Notebook

  •0•0•0•0•Updated Mar 11, 2022Mar 11, 2022

• tb_antibiogram

  Public
  R

  •0•0•0•0•Updated Sep 7, 2021Sep 7, 2021

• mtb-popstruct-2020

  Public
  R

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Aug 2, 2021Aug 2, 2021

• resdata

  Public
  Python

  •3•2•0•0•Updated Jul 1, 2021Jul 1, 2021

• fast-lineage-caller

  Public
  mycobacterium-tuberculosislineage-call

  Python

  •

  GNU General Public License v3.0

  •4•13•2•0•Updated Jun 30, 2021Jun 30, 2021

• resdata-ng

  Public
  DB of MTB resistance data and isolate metadata

  Python

  •1•6•6•0•Updated Oct 28, 2020Oct 28, 2020

• EVcouplings

  Public
  Evolutionary couplings from protein and RNA sequence alignments

  Jupyter Notebook

  •

  Other

  •76•0•0•0•Updated May 4, 2020May 4, 2020

• GenotypeTools

  Public
  Python code for reading, writing, and analyzing genotypes in various file formats

  Python

  •0•1•0•0•Updated Feb 19, 2020Feb 19, 2020

• geo_dist_tb

  Public
  Place to store code used for manuscript

  Python

  •0•0•0•0•Updated Jan 12, 2020Jan 12, 2020

• wdnn

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

  Python

  •13•14•4•2•Updated Dec 9, 2019Dec 9, 2019

• metatools_ncbi

  Public
  Download biosample and SRA runinfo metadata from NCBI

  Python

  •0•3•2•0•Updated Oct 31, 2019Oct 31, 2019

• fast-lineage-caller-vcf

  Public
  Python

  •2•4•0•0•Updated Sep 24, 2019Sep 24, 2019

• Non-tuberculous-Mycobacteria-Chart-Review

  Public
  Variable extraction for partners health system .txt file format database to dataframe for analysis in python or R.

  Python

  •1•0•0•0•Updated Apr 15, 2019Apr 15, 2019

• peru_cluster

  Public
  Code used for analysis of Peru cluster

  R

  •0•0•0•0•Updated Apr 12, 2019Apr 12, 2019

• analysis_pipeline

  Public
  Pipeline that takes user country-lineage-drug queries and output SNP alignment/BEAST tree output

  Python

  •0•0•0•0•Updated Jul 23, 2018Jul 23, 2018

• Stefans_Skript

  Public
  Python

  •0•0•0•0•Updated Jun 26, 2018Jun 26, 2018

• pyfasta

  Public
  fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

  Python

  •26•0•0•0•Updated Dec 11, 2017Dec 11, 2017

• vrt-tools

  Public
  Python

  •0•1•0•0•Updated Oct 5, 2017Oct 5, 2017