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@chan-csu Chan Lab at Colorado State University

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    21 repositories

    • SPAM-DFBA

      Public
      Formal repository for "Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution"
      HTML
      •3•6•0•0•Updated Mar 24, 2025Mar 24, 2025

    • ADToolbox

      Public
      AD Toolbox: A python package for modeling and optimization on anaerobic digestion process
      HTML
      •2•6•0•0•Updated Dec 10, 2024Dec 10, 2024

    • RCJ_Megtagenomics

      Public
      A New Repository for RCE Metagenomics Project
      HTML
      •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

    • inhouseCobraFunctions

      Public
      Some in-house matlab functions compatible with the COBRA toolbox
      MATLAB
      •0•0•1•0•Updated Mar 14, 2023Mar 14, 2023

    • OptForce_Bdoh

      Public
      A repository for bdoh over production work
      MATLAB
      •0•3•1•0•Updated Mar 3, 2022Mar 3, 2022

    • PyADM1

      Public
      PyADM1: a Python implementation of Anaerobic Digestion Model number 1
      Python
      •
      MIT License
      •24•1•0•0•Updated Jul 13, 2021Jul 13, 2021

    • spades

      Public
      SPAdes Genome Assembler
      C++
      •159•0•0•0•Updated Mar 11, 2021Mar 11, 2021

    • nextflow_sourmash

      Public
      Groovy
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • YAMP

      Public
      YAMP: Yet Another Metagenomic Pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •30•0•0•0•Updated Feb 10, 2021Feb 10, 2021

    • mag

      Public
      Assembly and binning of metagenomes
      Nextflow
      •
      MIT License
      •147•0•0•0•Updated Feb 10, 2021Feb 10, 2021

    • ampliseq

      Public
      16S rRNA amplicon sequencing analysis workflow using QIIME2
      Nextflow
      •
      MIT License
      •146•0•0•0•Updated Feb 4, 2021Feb 4, 2021

    • modelEcnLggExoMetabolomes

      Public
      MATLAB
      •0•0•0•0•Updated Dec 11, 2020Dec 11, 2020

    • carveme

      Public
      CarveMe: genome-scale metabolic model reconstruction
      Python
      •
      Other
      •62•0•0•0•Updated May 30, 2020May 30, 2020

    • SteadyCom

      Public
      Computing the maximum growth rate of a microbial community at community steady-state
      MATLAB
      •1•0•0•0•Updated Feb 20, 2020Feb 20, 2020

    • BiomassMW

      Public
      Determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models
      MATLAB
      •1•0•0•0•Updated Feb 20, 2020Feb 20, 2020

    • BiomassMWpy

      Public
      Python
      •1•0•0•0•Updated Feb 13, 2020Feb 13, 2020

    • spatialGut

      Public
      spatialGut: simulating the longitudinally and radially varying gut microbiota composition
      MATLAB
      •1•0•0•0•Updated Feb 7, 2020Feb 7, 2020

    • lll-FVA

      Public
      MATLAB
      •1•0•0•0•Updated Feb 7, 2020Feb 7, 2020

    • modelsChan2017

      Public
      The 20 curated models published in Chan et al., 2017, Bioinformatics
      0•0•0•0•Updated Feb 6, 2020Feb 6, 2020

    • NECom-FShaP

      Public
      MATLAB
      •
      Other
      •0•0•0•0•Updated Aug 24, 2019Aug 24, 2019

    • Tychus

      Public
      MIT License
      •9•0•0•0•Updated Feb 28, 2018Feb 28, 2018