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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 76 35

  2. curatedMetagenomicData curatedMetagenomicData Public

    Curated Metagenomic Data of the Human Microbiome

    R 162 32

  3. curatedTCGAData curatedTCGAData Public

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

    R 46 11

  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 7 9

  6. BugSigDB BugSigDB Public

    A microbial signatures database

    PHP 9 10

Repositories

Showing 10 of 127 repositories
  • BugSigDBExports Public

    BugSigDB data files

    waldronlab/BugSigDBExports's past year of commit activity
    R 5 4 9 3 Updated Nov 14, 2026
  • curatedTCGAData Public

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

    waldronlab/curatedTCGAData's past year of commit activity
    R 46 11 8 2 Updated Nov 13, 2026
  • BugSigDB Public

    A microbial signatures database

    waldronlab/BugSigDB's past year of commit activity
    PHP 9 10 12 3 Updated Nov 13, 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 9 2 Updated Nov 13, 2026
  • BugSigDBStats Public

    BugSigDB Stats and Analysis

    waldronlab/BugSigDBStats's past year of commit activity
    HTML 2 5 3 0 Updated Nov 13, 2026
  • CPTACdata Public
    waldronlab/CPTACdata's past year of commit activity
    R 0 0 0 0 Updated Nov 12, 2026
  • bugphyzzExports Public
    waldronlab/bugphyzzExports's past year of commit activity
    Python 1 1 9 0 Updated Nov 12, 2026
  • bugphyzzAnalyses Public

    Analyses with data and signatures imported from the bugphyzz package.

    waldronlab/bugphyzzAnalyses's past year of commit activity
    R 1 1 2 0 Updated Nov 12, 2026
  • bugphyzz Public

    Harmonized annotation of microbial physiology

    waldronlab/bugphyzz's past year of commit activity
    R 6 5 17 0 Updated Nov 12, 2026
  • taxPProValidation Public

    Code for validation analyses for prediction of annotations in bugphyzz

    waldronlab/taxPProValidation's past year of commit activity
    R 0 0 4 0 Updated Nov 12, 2026
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