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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

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 76 35

  2. curatedMetagenomicData curatedMetagenomicData Public

    Curated Metagenomic Data of the Human Microbiome

    R 160 32

  3. curatedTCGAData curatedTCGAData Public

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

    R 46 10

  4. cBioPortalData cBioPortalData Public

    Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

    R 37 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 123 repositories
  • BugSigDBExports Public

    BugSigDB data files

    waldronlab/BugSigDBExports's past year of commit activity
    R 5 4 8 0 Updated Sep 10, 2026
  • BugSigDBStats Public

    BugSigDB Stats and Analysis

    waldronlab/BugSigDBStats's past year of commit activity
    HTML 2 5 5 0 Updated Sep 10, 2026
  • czieoss6-biocgpu Public

    Website tracking repositories related to czieoss6-biocgpu

    waldronlab/czieoss6-biocgpu's past year of commit activity
    0 0 0 0 Updated Sep 10, 2026
  • curatedMetagenomicDataCuration Public

    Sample Metadata Curation for curatedMetagenomicData

    waldronlab/curatedMetagenomicDataCuration's past year of commit activity
    R 32 26 27 (2 issues need help) 3 Updated Sep 9, 2026
  • BugSigDB Public

    A microbial signatures database

    waldronlab/BugSigDB's past year of commit activity
    PHP 8 8 19 4 Updated Sep 9, 2026
  • CNVRanger Public

    Functionality for CNV analysis

    waldronlab/CNVRanger's past year of commit activity
    R 8 7 13 0 Updated Sep 8, 2026
  • bioanalyzer-backend Public

    Streamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from research papers, reducing manual curation time and improving data quality for the BugSigDB database.

    waldronlab/bioanalyzer-backend's past year of commit activity
    Python 2 MIT 0 3 2 Updated Sep 1, 2026
  • MultiAssayExperiment Public

    Bioconductor package for management of multi-assay data

    waldronlab/MultiAssayExperiment's past year of commit activity
    R 76 35 0 0 Updated Aug 28, 2026
  • ai-agent-protocols Public

    Citable scientific protocols for use by AI agents

    waldronlab/ai-agent-protocols's past year of commit activity
    R 3 MIT 1 5 2 Updated Aug 19, 2026
  • curator-desk Public

    Curator dashboard for reviewing BioAnalyzer predictions — sortable table, field-level feedback, submit via GitHub Issues

    waldronlab/curator-desk's past year of commit activity
    R 0 0 4 0 Updated Aug 16, 2026