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  • UW Madison Statistics Department
  • Madison, WI

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Achievement: Pull SharkAchievement: QuickdrawAchievement: Arctic Code Vault Contributor

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  • cbreenmachine.github.io Public

    Forked from academicpages/academicpages.github.io

    Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

    JavaScript MIT License Updated Sep 28, 2024

  • Sequence2Methylation-v1-preprocessing Public

    Running the scripts to encode variants, filter by coverage, and standardize covariates.

    Jupyter Notebook MIT License Updated Aug 10, 2024

  • methy-process-v2 Public

    A re-write of the whole-genome methylation sequencing processing pipeline.

    MIT License Updated Aug 9, 2024

  • 850k-BMI Public

    Scripts used to analyze EPIC 850k arrays for associations with BMI

    R MIT License Updated Mar 15, 2024

  • 240312-seq-stats Public

    Compute summary statistics for aligned sequencing files.

    MIT License Updated Mar 12, 2024

  • seq-to-methy-public-data Public

    Processing meQTL, interactions, etc.

    MIT License Updated Jan 9, 2024

  • vencoder Public

    Python module to encode variants in a variety of schemes.

    Python MIT License Updated Jan 3, 2024

  • meAD-paper Public

    Analysis of methylation data from Late-onset AD cohort

    R Updated Nov 28, 2023

  • genplot Public

    Miscellaneous genomics plots

    R MIT License Updated Nov 6, 2023

  • deep-learning-sandbox Public

    Notebooks to demonstrate basic deep learning concepts.

    MIT License Updated Oct 2, 2023

  • meAD-UCSC-tracks Public

    Updated Sep 29, 2023

  • meAD-models-targets Public

    Targeted version of meAD-models pipeline

    R MIT License Updated Sep 26, 2023

  • meAD-models Public

    R Updated Sep 18, 2023

  • HPC-notes Public

    Notes from Dan Negrut's High-Performance Computing Class (ME 759)

    MIT License Updated Sep 18, 2023

  • safe-haven Public

    Some notebooks to convince myself of concepts from Spitznagel's "Safe Haven"

    Updated Aug 13, 2023

  • snv-methy-preprocessing Public

    EDA and prototyping

    Jupyter Notebook MIT License Updated Aug 10, 2023

  • methy-seq-gemBS-processing Public

    Rewrite of methylation processing pipeline using snakemake

    Python MIT License Updated Jul 12, 2023

  • meAD-850k Public

    R Updated May 13, 2023

  • me-hc-bayes Public

    R MIT License Updated Dec 15, 2022

  • axonregen Public

    HTML Updated Dec 8, 2022

  • meAD-fq2bed Public

    Pipeline used to take raw fastq files, trim, map, and process to methylated / coverage bed files

    Shell Updated Nov 27, 2022

  • volplot Public

    Volcano plot

    R Updated Nov 25, 2022

  • goplot Public

    R Updated Nov 25, 2022

  • eda-meQTL Public

    Quick exploratory analysis of meQTL in LOAD project

    MIT License Updated Nov 15, 2022

  • badger Public

    R Updated Nov 5, 2022

  • LOAD-850k-analysis Public

    R Updated Aug 14, 2022

  • LOAD-DMPs-browser Public

    R Updated Aug 1, 2022

  • RNAseqElegans Public

    Updated May 16, 2022

  • methy-load Public

    HTML 2 MIT License Updated Mar 8, 2022

  • Rray Public

    Idioms and workflows used frequently in EPIC 850K array analysis

    R Updated Feb 21, 2022