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    15 repositories

    • DRAM

      Public
      Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
      bioinformaticsannotationgenomicsmetagenomicsmicrobiomeviral-genomicsviral-metagenomicsmetagenome-assembled-genomes
      Python
      •
      GNU General Public License v3.0
      •57•306•118•2•Updated Dec 15, 2025Dec 15, 2025

    • server-scripts

      Public
      Central location for tools and scripts for the lab
      Python
      •0•0•0•0•Updated Oct 18, 2025Oct 18, 2025

    • dram-viz

      Public
      A library for visualizing the output of DRAM v2
      Python
      •
      MIT License
      •0•1•2•0•Updated Jul 30, 2025Jul 30, 2025

    • catechin_incubations

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • JGI-API-Request

      Public
      Python script is designed to fetch and process genomic data from the Joint Genome Institute (JGI) API, allowing users to request file downloads programmatically based on given taxon IDs.
      Python
      •1•4•0•0•Updated Jul 2, 2024Jul 2, 2024

    • Protpipeliner

      Public
      This script combines MUSCLE, GBLOCKS, Prottest and RaxML for an efficient and streamlined method of building trees.
      Python
      •0•1•0•0•Updated May 14, 2024May 14, 2024

    • CAMPER

      Public
      This is a repository for CAMPER.
      Python
      •
      GNU General Public License v3.0
      •0•15•2•0•Updated Mar 18, 2024Mar 18, 2024

    • stordalen_polyphenols_paper

      Public
      HTML
      •0•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • AD_CERC

      Public
      0•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • kb_DRAM

      Public
      A Kbase app for DRAM
      Python
      •
      MIT License
      •3•1•3•0•Updated Jun 24, 2023Jun 24, 2023

    • prodigal-recoding

      Public
      Fork of Prodigal Gene Prediction Software to introduce recoding of stop codons
      C
      •
      GNU General Public License v3.0
      •93•0•0•0•Updated Apr 1, 2023Apr 1, 2023

    • join_asvbins

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Dec 8, 2022Dec 8, 2022

    • emerge_pipline

      Public
      The pipline for the folks at emerge, they will want it eventualy
      Python
      •2•0•0•0•Updated Aug 29, 2022Aug 29, 2022

    • columbia_river

      Public
      GitHub Repository of code used for the publication titled: Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 1, 2022Jun 1, 2022

    • sporulation_utils

      Public
      These tools help us study sporulation AMGs with DRAM-v and DRAM
      Python
      •1•0•0•0•Updated Feb 15, 2022Feb 15, 2022