Package: SMTrackR 1.1.0

Satyanarayan Rao

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

The package uses exogenous enzyme imprinted information to map protein-DNA binding on individual sequenced DNA molecules. For example, GpC methyltransferase, CpG methyltransferase, and Adenine methyltransferases. Public datasets from such assays are compiled into tracks, and hosted at public servers like Galaxy for their seamless access by this package.

Authors:Aashna Bansal [aut, ctb], Himani Barmola [aut, ctb], Shivam Yadav [aut, ctb], Satyanarayan Rao [aut, cre]

SMTrackR_1.1.0.tar.gz
SMTrackR_1.1.0.zip(r-4.7)SMTrackR_1.1.0.zip(r-4.6)SMTrackR_1.1.0.zip(r-4.5)
SMTrackR_1.1.0.tgz(r-4.6-any)SMTrackR_1.1.0.tgz(r-4.5-any)
SMTrackR_1.1.0.tar.gz(r-4.7-any)SMTrackR_1.1.0.tar.gz(r-4.6-any)
SMTrackR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SMTrackR/json (API)
NEWS

# Install 'SMTrackR' in R:

install.packages('SMTrackR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/satyanarayan-rao/smtrackr/issues

On BioConductor:SMTrackR-1.1.0(bioc 3.24)SMTrackR-1.0.0(bioc 3.23)

nucleosomepositioning visualization genetarget genomeassembly

4.90 score 2 scripts 145 downloads 6 exports 79 dependencies

Last updated from:bff9c40d94. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	189
linux-devel-x86_64	NOTE	365
source / vignettes	OK	282
linux-release-x86_64	NOTE	362
macos-release-arm64	NOTE	266
macos-oldrel-arm64	NOTE	198
windows-devel	NOTE	277
windows-release	NOTE	306
windows-oldrel	NOTE	291
wasm-release	OK	150

Exports:generateGvizCodeforSMF listTracks plotFootprints plotFootprintsUsingLocalBigBed plotMethylationCallsNanopore plotMethylationCallsNanoporeUsingLocalBigBed

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue httr httr2 IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XML XVector yaml

SMTrackR

Aashna Bansal, Himani Barmola, Shivam Yadav, Satyanarayan Rao

Rendered fromreference_manual.rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2026-04-24
Started: 2025-06-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Visualize Single Molecule Footprint Patterns with Ideogram and Gene Tracks	generateGvizCodeforSMF
Discover Available Single Molecule Data Tracks	listTracks
Visualize Single Molecule Footprint Patterns	plotFootprints
Visualize Single Molecule Footprint Patterns using Local BigBed file	plotFootprintsUsingLocalBigBed
Visualize Single Molecule Footprint Patterns	plotMethylationCallsNanopore
Visualize aggregate methylation calls from ONT sequencing data	plotMethylationCallsNanoporeUsingLocalBigBed