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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

    R

  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

Showing 10 of 14 repositories
  • 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 with the BCB-SR Bioinformatics unit, using the command line, finding gold-standard tools, and trouble-shotting common challenges.

    UFHCC-BCBSR/res-hub’s past year of commit activity
    HTML 0 0 2 0 Updated Oct 14, 2025
  • .github Public
    UFHCC-BCBSR/.github’s past year of commit activity
    0 0 0 0 Updated Oct 14, 2025
  • res-bioinfo-showcase Public

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

    UFHCC-BCBSR/res-bioinfo-showcase’s past year of commit activity
    JavaScript 0 0 0 0 Updated Oct 14, 2025
  • app-rnareportR Public

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

    UFHCC-BCBSR/app-rnareportR’s past year of commit activity
    R 0 0 5 0 Updated Oct 14, 2025
  • app-deeptools-plot Public

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

    UFHCC-BCBSR/app-deeptools-plot’s past year of commit activity
    R 0 0 0 0 Updated Oct 6, 2025
  • app-batch-corrector Public

    batch correction app with comBat and comBat-seq

    UFHCC-BCBSR/app-batch-corrector’s past year of commit activity
    R 0 0 0 0 Updated Sep 26, 2025
  • 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.

    UFHCC-BCBSR/app-atacreportR’s past year of commit activity
    R 0 0 2 0 Updated Sep 25, 2025
  • 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.

    UFHCC-BCBSR/app-washu-hubhelper’s past year of commit activity
    R 0 0 1 0 Updated Sep 16, 2025
  • atac-reportR Public archive

    A portable shiny app version of the nextflow atacreport module

    UFHCC-BCBSR/atac-reportR’s past year of commit activity
    HTML 0 0 5 0 Updated Sep 4, 2025
  • app-clouperator Public

    clouperator converts Seurat objects from R into .cloupe files that can be visualized in 10X Genomics Loupe Browser. This allows you to explore your single-cell data interactively with 10X's powerful visualization tools.

    UFHCC-BCBSR/app-clouperator’s past year of commit activity
    R 0 0 0 0 Updated Sep 3, 2025
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