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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 126 repositories
  • BugSigDBExports Public

    BugSigDB data files

    waldronlab/BugSigDBExports's past year of commit activity
    R 5 4 8 0 Updated Nov 11, 2026
  • BugSigDBStats Public

    BugSigDB Stats and Analysis

    waldronlab/BugSigDBStats's past year of commit activity
    HTML 2 5 5 0 Updated Nov 11, 2026
  • bugphyzzExports Public
    waldronlab/bugphyzzExports's past year of commit activity
    Python 1 1 8 1 Updated Nov 11, 2026
  • bugphyzz Public

    Harmonized annotation of microbial physiology

    waldronlab/bugphyzz's past year of commit activity
    R 6 5 15 1 Updated Nov 11, 2026
  • bugphyzzAnalyses Public

    Analyses with data and signatures imported from the bugphyzz package.

    waldronlab/bugphyzzAnalyses's past year of commit activity
    R 1 1 1 0 Updated Nov 11, 2026
  • agent-protocol-standard Public

    Standard to define citable scientific protocols for use by AI agents

    waldronlab/agent-protocol-standard's past year of commit activity
    Python 5 MIT 2 17 0 Updated Nov 10, 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 9, 2026
  • cBioPortalData Public

    Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

    waldronlab/cBioPortalData's past year of commit activity
    R 37 13 5 0 Updated Nov 9, 2026
  • bugSigSimple Public

    Simple exploratory analysis of curated microbe signatures

    waldronlab/bugSigSimple's past year of commit activity
    R 4 18 2 (2 issues need help) 0 Updated Nov 9, 2026
  • bedbaser Public

    An R client for bedbase.org

    waldronlab/bedbaser's past year of commit activity
    R 3 2 5 0 Updated Nov 7, 2026
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