UFHCC BCB-SR In-House Tools
The UF Health Cancer Center Bioinformatics team develops and maintains a growing set of in-house tools designed to support clinical, translational, and basic science research. These tools help streamline data analysis, automate reporting, and enhance reproducibility across omics workflows.
This page links to documentation, usage guides, and public versions of our internal apps and scripts. Whenever possible, we provide options for local deployment or access through HiPerGator.
Contact the Bioinformatics team to request access or collaboration on tool extension.
Applications
Our Applications
Tools developed and maintained by the UFHCC BCB-SR team for reproducible omics data analysis
- DECODeR — Differential Exploration of Counts-based Omics Data in R. Analysis and visualization of counts data derived from bulk RNA-seq or related assays
- HeatPath — Instantly generate gene expression heatmaps from your uploaded RNA-seq counts by searching pathway databases or uploading lists of pathways
- ClusterPicker — Interactively explore and extract gene clusters from heatmaps
- atacreportR — Generate a comprehensive differential analysis and interactive report from the output of nf-core/atacseq. This is only available on the UF network. Contact our team for access
- rnareportR — Generate a comprehensive differential analysis and interactive report from the output of nf-core/rnaseq. This is only available on the UF network. Contact our team for access
- CloupeRator — Upload a processed Seurat object and download a .cloupe file that can then be imported into the 10X Loupe Browser v7.0 for data visualization and further exploration
Project Management Tools
Internal tools for project tracking and workflow management
- BCB-SR Project Tracker — Internal project tracking dashboard
- Care2 Inventory — CARE2 project metadata inventory
Hosted Applications
External tools hosted locally for enhanced security and performance compared to public servers
- Icarus — Single-cell data visualization
- ExpressAnalyst — Gene expression analysis from raw fastq.gz files