SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules

Motivation: Single-molecule assays like NOMe-seq, dSMF, and Nanopore are superior to DNase-seq and ATAC-seq as they do not destroy DNA. Thus, they enable quantification of all three, that is, protein-free, Transcription Factor-bound, and histone-complex-bound states. But a user-friendly tool to visualize and quantify such states is lacking. Here, we present SMTrackR, an R/Bioconductor package to visualize protein-DNA binding states on individual sequenced DNA molecules. Results: SMTrackR queries the single-molecule footprint database we built and hosted at Galaxy Server. It comprises BigBed files generated from NOMe-seq, dSMF, and Nanopore (SMAC-seq) datasets. SMTrackR exploits UCSC REST API to query a BigBed file and plot footprint heatmap categorized in different binding states, as well as report their occupancies. Additionally, this package generates a Gviz-enabled script to visualize these single molecules on gene tracks. Availability and implementation: The SMTrackR tool is implemented in the statistical programming language R and is available as a Bioconductor package, SMTrackR (https://bioconductor.org/packages/3.23/bioc/html/SMTrackR.html). The GitHub repository at https://github.com/satyanarayan-rao/SMTrackR has latest updates. The installation time is less than five minutes given the dependent packages are installed. The tool is also available as a web version https://smtrackrest.iitr.ac.in/. A function is provided to use local BigBed file for users who wish to use unpublished data. A fully automated pipeline to generate such BigBed files is available at https://github.com/satyanarayan-rao/SMF_for_SMThub, and https://github.com/satyanarayan-rao/dSMF_for_SMThub.