Welcome to the Ruggles Lab GitHub repository! Led by Dr. Kelly Ruggles, our lab at NYU focuses on computational multi-omics to advance understanding of human health, with applications in cancer, inflammation, and cardiovascular disease. We apply data integration, visualization, and predictive modeling to diverse data types, including genomic, proteomic, metabolomic, and microbiome data, as well as clinical trial and behavioral data.
Explore our public repositories for tools and resources developed by our lab:
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MelOD: The Melanoma Omics Dashboard (MelOD) is a tool for visualizing and analyzing melanoma-related omics data.
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HyperCluster: A Python package and Snakemake workflow for parallelized clustering optimization.
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BlackSheep: A tool for differential extreme-value analysis with packages in both Python and R.
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WHAM!: The Workflow Hub for Automated Metagenomic Exploration (WHAM!) is an RShiny web tool for exploratory analysis of metagenomic and metatranscriptomic data.
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RIVET: Ribosomal Investigation and Visualization to Evaluate Translation (RIVET) is a tool to automate the statistical analysis of RNA-seq data from polysome profiling or ribosome footprinting experiments.
For more information about our projects and publications, visit our lab website.
We welcome collaboration and encourage you to explore our repositories.