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    21 repositories

    • FimTyper

      Public
      Perl
      •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • ClermonTyping

      Public
      Clermont PCR method In-Silico
      Python
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated May 17, 2025May 17, 2025

    • 2023_Blake_TrEAT-PREVENT-TD

      Public
      Data, code, and analyses for Blake, Schwartz, Paruthiyil et al. (2023). mBio. PMID: 38085102.
      Shell
      •1•0•0•0•Updated Apr 22, 2025Apr 22, 2025

    • ICUSink

      Public
      Scripts used for analysis in the ICU Sink project.
      Python
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • preclinAD_GutMicrobiomes

      Public
      Analyses of stool microbiomes from preclinical Alzheimer disease cohorts
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 10, 2025Mar 10, 2025

    • 2024_Blake_TET-resistome

      Public
      Data, code, and analyses for Blake (2024). Nature Communications.
      HTML
      •1•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • 2024_Fishbein_DeVeaux_Khanna_Cdiff_DefCom_Microbiome

      Public
      Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization
      R
      •0•0•0•0•Updated Dec 15, 2024Dec 15, 2024

    • 2024_Sb_Probiotics_CancerMicrobiome

      Public
      R Script to analyze and visualize 16S amplicon data included in Gorushi, Wallace, and Prusa 2024
      R
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • spack-gdlab-repo

      Public
      Dantas Lab's custom spack packages
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Aug 29, 2024Aug 29, 2024

    • deconseq-multi

      Public
      Modified Deconseq to utilize multiple threads
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • NICUExposome

      Public
      Scripts for NICU Exposome manuscript
      R
      •0•1•0•0•Updated Jul 13, 2024Jul 13, 2024

    • .github

      Public
      0•0•0•0•Updated Jul 8, 2024Jul 8, 2024

    • spack

      Public
      A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
      Python
      •
      Other
      •2.4k•0•0•0•Updated Jun 29, 2024Jun 29, 2024

    • 2023_Blake_TDase-HMM-mut

      Public archive
      Data, code, and analyses for Blake et al. (2023). Commun Biol.
      Shell
      •1•0•0•0•Updated Feb 8, 2024Feb 8, 2024

    • DOME

      Public
      R
      •0•1•0•0•Updated Oct 19, 2023Oct 19, 2023

    • 2023_Talat_India-HWW

      Public archive
      Data, code, and analyses for Talat & Blake et al. (2023). Microbiology Spectrum. PMID: 36786639.
      R
      •
      MIT License
      •2•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • parfums

      Public
      Perl
      •
      MIT License
      •2•0•0•0•Updated Oct 27, 2022Oct 27, 2022

    • resAnnotator

      Public
      Python
      •
      MIT License
      •0•3•1•0•Updated Oct 27, 2022Oct 27, 2022

    • resfams_update

      Public
      Update to resfams database
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 10, 2020Jan 10, 2020

    • ngs-scripts

      Public
      Scripts to analyze high-throughput sequencing data
      Python
      •
      Other
      •0•0•0•0•Updated Apr 1, 2019Apr 1, 2019

    • resfams

      Public
      Antibiotic Resistance annotation by profile Hidden Markov Models
      0•3•2•0•Updated Feb 27, 2018Feb 27, 2018