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@UFHCC-BCBSR

UF Health Cancer Center BCB-SR Bioinformatics

Bioinformatics pipelines, R/Shiny applications, and analysis tools from the UF Health Cancer Center BCB-SR team.
README.md

UF Health Cancer Center Bioinformatics

Welcome! We're the Biostatistics & Computational Biology Shared Resource at UF Health Cancer Center. This GitHub organization hosts our bioinformatics tools, analysis pipelines, and resources for cancer omics research.

What You'll Find Here

Our repositories follow a naming convention to help you navigate:

  • Shiny Applications (app-*) - Interactive web tools for omics data analysis and visualization
  • Analysis Pipelines (cb-*) - Reproducible workflows for RNA-seq, ATAC-seq, and other omics data
  • Resources (res-*) - Presentations, workshops, and educational materials
  • R Packages (pkg-*) - Installable packages for bioinformatics analysis
  • Project Repositories (proj-pi-*) - Collaborative research projects

Browse by topics to find repos by data type (rna-seq, atac-seq) or category (shiny-apps, manuscript, codebase).

More Information

Contact

Questions about our tools or interested in collaboration? Reach out through the UF Health Cancer Center Biostatistics & Computational Biology Shared Resource.

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  1. app-rnareportR app-rnareportR Public

    Rmarkdown DE analysis reporting module post nf-core/rnaseq pipeline

    HTML

  2. app-atacreportR app-atacreportR Public

    A Shiny application for performing differential accessibility analysis of consensus peaks' count data on HiPerGator storage and/or preparing peak data and bam files for such an analysis.

    R

  3. app-deeptools-plot app-deeptools-plot Public

    A Shiny application for creating deeptools plots (heatmap, profile) from bigwigs and bed files in HiPerGator storage

    R

  4. app-washu-hubhelper app-washu-hubhelper Public

    A Shiny application for generating and hosting datahub.json files compatible with the WashU Epigenome Browser from HiPerGator /blue storage and to the HiPerGator static file server.

    R

  5. res-bioinfo-showcase res-bioinfo-showcase Public

    Management of prep, materials, and links for the UFHCC BCB-SR Bioinformatics showcase on Sept. 3, 2025

    JavaScript

  6. res-hub res-hub Public

    The UFHCC BCB-SR Bioinformatics hub is where we BCB-SR Bioinformatics members collaboratively document how to navigate bioinformatics in the UF Health Cancer Center (and beyond) from collaborating …

    HTML

Repositories

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