ArticleBioinformatics advances2026
SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.