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  • GT-micro-metabo Public

    Microbiome-metabolome interactions in mice consuming green tea (IQ Bio rotation with Nichole Reisdorph)

    Jupyter Notebook Updated Sep 27, 2024

  • HoMi Public

    Host-microbiome dual transcriptome pipeline

    Python Other Updated Sep 23, 2024

  • sterrettJD.github.io Public

    Updated Sep 21, 2024

  • gpLM-reading-group Public

    2 Updated Sep 11, 2024

  • Glutenshield Public

    Pre + pro-biotic trial

    Shell Updated Jul 30, 2024

  • EPSS Public

    Shell Updated Jul 19, 2024

  • HoMiStats Public

    Statistics for host-microbiome dual transcriptomics

    R Updated Apr 26, 2024

  • Effective-Snakemake-HPC Public

    Resource for effectively using Snakemake on high performance compute clusters, with applications to metagenomics

    CSS Updated Apr 22, 2024

  • CauDA Public

    Using knowledge to improve differential abundance testing

    R Other Updated Jan 4, 2024

  • poly-omics-risk Public

    R Updated Nov 20, 2023

  • bit Public

    Forked from AstrobioMike/bit

    Bioinformatics Tools

    Python GNU General Public License v3.0 Updated Oct 10, 2023

  • microbiome-disco-sandbox Public

    Sandbox for learning some git/github and microbiome data processing simultaneously

    Updated Oct 4, 2023

  • Phadtare-IBS Public

    Irritable Bowel Syndrome microbiome/metabolome analysis in individuals from Camden, NJ

    HTML Updated Oct 3, 2023

  • HIV-microbiome Public

    Gut microbiome of HIV+ individuals in rural Appalachia

    Jupyter Notebook Updated Sep 27, 2023

  • microshades Public

    Forked from KarstensLab/microshades

    This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions for applying these colors to microbiome data.

    R Other Updated Jul 27, 2023

  • HIV-MetaG Public

    Python Updated Jun 23, 2023

  • Log-ratio-subcomp Public

    Updated Jun 8, 2023

  • Breastfed-Neonates Public

    Analysis of microbiomes of breastfeed infants from Camden, New Jersey

    Jupyter Notebook 1 Updated Feb 26, 2023

  • quast Public

    Forked from ablab/quast

    Genome assembly evaluation tool

    AMPL Other Updated Feb 21, 2023

  • AoC-2022 Public

    Advent of code 2022

    Julia Updated Dec 11, 2022

  • Chemobrain Public

    Analysis of gut microbiome of chemotherapy patients with cognitive dysfunction

    Jupyter Notebook Updated Oct 24, 2022

  • Diff-abundance-tool Public

    Simple microbiome differential abundance using STAN

    R Updated Sep 20, 2022

  • ymp Public

    Forked from epruesse/ymp

    Flexible omics pipeline

    Python GNU General Public License v3.0 Updated Aug 31, 2022

  • IQ2022Rosalind Public

    Teaching repository for IQ Bio 2022 Bootcamp

    1 Updated Aug 16, 2022

  • q2-longitudinal Public

    Forked from qiime2/q2-longitudinal

    QIIME 2 plugin for paired sample comparisons

    Python BSD 3-Clause "New" or "Revised" License Updated Jul 14, 2022

  • Multi-omics-tools Public

    Tools for multi-omics analyses

    Python Updated Feb 22, 2022

  • CU-Sewer-Metagenomics Public

    Analysis of CU Boulder sewer system metagenome (from sampling effort for SARS-CoV2 detection) focused on temporal patterns

    Jupyter Notebook Updated Jan 26, 2022

  • Nicotine-Microbiome Public

    IQ Biology Rotation Project with Noah Fierer

    Jupyter Notebook Updated Dec 15, 2021

  • CSCI-6118-Project Public

    An Interactive Educational Resource for the Analysis of Microbial Community Ecology

    Jupyter Notebook 1 1 Updated Dec 11, 2021

  • twitterscraper Public

    Forked from taspinar/twitterscraper

    Scrape Twitter for Tweets

    Python MIT License Updated Nov 22, 2021