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@waldronlab

Waldron Lab at the CUNY SPH

Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City
README.md

Waldron Lab

Welcome to the Waldron lab for public health data science at the CUNY School of Public Health in New York City. I, Levi Waldron, teach biostatistics, have an active research program in cancer genomics and in metagenomic profiling of the human microbiome, develop methods within the intersection of statistical analysis and computation, and work to develop an inclusive community of researchers and students around open-source bioinformatics software and methods. My lab aims to generate new insights into human health, disease, and treatment through improved tools and novel analysis of publicly available data. I welcome anyone to get involved and join active communities working on BugSigDB: A Comprehensive Database of Microbial Signatures and the Microbiome Virtual International Forum.

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  1. MultiAssayExperiment MultiAssayExperiment Public

    Bioconductor package for management of multi-assay data

    R 73 34

  2. curatedMetagenomicData curatedMetagenomicData Public

    Curated Metagenomic Data of the Human Microbiome

    R 151 31

  3. curatedTCGAData curatedTCGAData Public

    Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

    R 44 9

  4. cBioPortalData cBioPortalData Public

    Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

    R 34 13

  5. presentations presentations Public

    A repository for public presentations

    TeX 6 9

  6. BugSigDB BugSigDB Public

    A microbial signatures database

    PHP 8 8

Repositories

Showing 10 of 118 repositories
  • czieoss6-biocgpu Public

    Website tracking repositories related to czieoss6-biocgpu

    waldronlab/czieoss6-biocgpu’s past year of commit activity
    0 0 0 0 Updated Mar 28, 2026
  • BugSigDBExports Public

    BugSigDB data files

    waldronlab/BugSigDBExports’s past year of commit activity
    R 3 4 5 1 Updated Mar 27, 2026
  • config Public

    A repository for common configuration scripts

    waldronlab/config’s past year of commit activity
    Shell 0 0 0 0 Updated Mar 27, 2026
  • repo-audits Public
    waldronlab/repo-audits’s past year of commit activity
    R 0 0 0 0 Updated Mar 27, 2026
  • waldronlab.r-universe.dev Public

    https://waldronlab.r-universe.dev/

    waldronlab/waldronlab.r-universe.dev’s past year of commit activity
    0 0 0 0 Updated Mar 26, 2026
  • TCGAutils Public

    Toolbox package for organizing and working with TCGA data

    waldronlab/TCGAutils’s past year of commit activity
    R 28 7 1 0 Updated Mar 26, 2026
  • bedbaser Public

    An R client for bedbase.org

    waldronlab/bedbaser’s past year of commit activity
    R 2 2 5 0 Updated Mar 26, 2026
  • terraTCGAdata Public

    TCGA data access on Terra

    waldronlab/terraTCGAdata’s past year of commit activity
    R 0 0 0 0 Updated Mar 26, 2026
  • lefser Public

    R implementation of the LEfSe method

    waldronlab/lefser’s past year of commit activity
    R 64 7 8 1 Updated Mar 26, 2026
  • HMP16SData Public

    16S rRNA Sequencing Data from the Human Microbiome Project

    waldronlab/HMP16SData’s past year of commit activity
    R 10 6 0 0 Updated Mar 26, 2026
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