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✨
DESCRIPTION |NEWS
card.svg |card.png
SMTrackR/json (API)

# 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

4.85 score 2 scripts 6 exports 79 dependencies

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

Target	Result	Time
bioc-checks	NOTE	203
linux-devel-x86_64	NOTE	358
source / vignettes	OK	302
linux-release-x86_64	NOTE	395
macos-release-arm64	NOTE	209
macos-oldrel-arm64	NOTE	189
windows-devel	NOTE	284
windows-release	NOTE	271
windows-oldrel	NOTE	247
wasm-release	OK	163

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

Rendered fromreference_manual.rmdusingknitr::rmarkdown

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