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    17 repositories

    • RAMP_study_analysis

      Public
      0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • NSG_mouse_metagenomics

      Public
      This repo contains data regarding analysis of a diarrhea outbreak among NSG mice at Stanford University
      0•0•0•0•Updated Aug 29, 2022Aug 29, 2022

    • aws-genomics-workflows

      Public
      Genomics Workflows on AWS
      Shell
      •
      MIT No Attribution
      •110•0•0•0•Updated Jun 17, 2022Jun 17, 2022

    • cblaster

      Public
      Find clustered hits from a BLAST search
      HTML
      •
      MIT License
      •24•0•0•0•Updated May 4, 2022May 4, 2022

    • project-probiotic-study

      Public
      Data and code for the Probiotic Study
      0•0•0•0•Updated Apr 27, 2022Apr 27, 2022

    • dbCAN_meta_server

      Public
      This repo contains code obtained from http://cys.bios.niu.edu/dbCAN2/download/
      Python
      •0•0•3•0•Updated Apr 8, 2022Apr 8, 2022

    • fiber-fermented-study

      Public
      HTML
      •5•7•1•0•Updated Jun 29, 2021Jun 29, 2021

    • Metabolomics_Data_Explorer

      Public
      JavaScript
      •0•5•0•0•Updated Jun 1, 2021Jun 1, 2021

    • Han_and_Van_Treuren_et_al_2021

      Public
      Jupyter Notebook
      •1•7•0•0•Updated Jun 1, 2021Jun 1, 2021

    • CAZy_Annotations

      Public
      Just a list of annotations for GHs and PLs. These are mostly pulled from cazypedia.org. These annotations are non-exclusive. For example, something can be annotated as animal carbohydrate degrading and HMO degrading. Feel free to add as you find new annotations.
      0•0•0•0•Updated Oct 22, 2020Oct 22, 2020

    • DIETFITS-AJCN

      Public
      0•0•0•0•Updated Oct 20, 2020Oct 20, 2020

    • PHISH

      Public
      PHages In SearcHsra
      0•0•0•0•Updated Feb 14, 2020Feb 14, 2020

    • run_dbcan

      Public
      Run_dbcan V2, using genomes/metagenomes/proteomes of any orgaisms(prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
      Python
      •
      GNU General Public License v3.0
      •41•0•0•0•Updated Feb 11, 2020Feb 11, 2020

    • drep

      Public
      Rapid comparison and dereplication of genomes
      Python
      •38•0•0•0•Updated Feb 2, 2020Feb 2, 2020

    • VirSorter

      Public
      Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
      Perl
      •
      GNU General Public License v2.0
      •30•0•0•0•Updated Dec 12, 2019Dec 12, 2019

    • lathe

      Public
      A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
      Python
      •
      MIT License
      •18•0•0•0•Updated Nov 9, 2019Nov 9, 2019

    • MAGpurify

      Public
      Improvement of metagenome-assembled genomes
      Python
      •
      GNU General Public License v3.0
      •12•1•0•0•Updated Nov 4, 2019Nov 4, 2019