SMTrackR

SMTrackR visualizes and quantifies protein-DNA binding states on single sequenced DNA molecules by querying a single-molecule footprint database and generating heatmap visualizations categorized by binding states.

Key Features:

• Database Querying: SMTrackR queries a single-molecule footprint database hosted at Galaxy Server comprising BigBed files generated from NOMe-seq, dSMF, and Nanopore (SMAC-seq) datasets.
• Heatmap Visualization: SMTrackR plots footprint heatmaps categorized by different binding states including protein-free, Transcription Factor-bound, and histone-complex-bound states.
• Occupancy Reporting: SMTrackR reports the occupancies of the different binding states.
• Gene Track Visualization: SMTrackR generates a Gviz-enabled script to visualize single molecules on gene tracks.
• Local File Support: SMTrackR provides a function to use local BigBed files for unpublished data.

Scientific Applications:

• Single-Molecule Footprint Analysis: SMTrackR enables analysis of protein-DNA binding at individual DNA molecules using NOMe-seq, dSMF, and Nanopore (SMAC-seq) data.
• Binding State Quantification: SMTrackR quantifies all three binding states: protein-free, Transcription Factor-bound, and histone-complex-bound states.

Methodology:

SMTrackR exploits the UCSC REST API to query BigBed files.