Package: methylscaper 1.21.0

Bacher Rhonda

methylscaper: Visualization of Methylation Data

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

Authors:Bacher Rhonda [aut, cre], Parker Knight [aut]

methylscaper_1.21.0.tar.gz
methylscaper_1.21.0.zip(r-4.7)methylscaper_1.21.0.zip(r-4.6)methylscaper_1.21.0.zip(r-4.5)
methylscaper_1.21.0.tgz(r-4.6-any)methylscaper_1.21.0.tgz(r-4.5-any)
methylscaper_1.21.0.tar.gz(r-4.7-any)methylscaper_1.21.0.tar.gz(r-4.6-any)
methylscaper_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
methylscaper/json (API)

# Install 'methylscaper' in R:
install.packages('methylscaper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rhondabacher/methylscaper/issues

Datasets:
  • human_bm - Human gene symbols and positions
  • mouse_bm - Mouse gene symbols and positions
  • reads_sm - Example reads from single-molecule experiment
  • ref_seq - Example reference sequence to align reads to from a single-molecule experiment
  • singlecell_subset - Example preprocessed single-cell experiment subset
  • singlemolecule_example - Example preprocessed single-molecule experiment

On BioConductor:methylscaper-1.21.0(bioc 3.24)methylscaper-1.20.0(bioc 3.23)

dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning

4.70 score 1 stars 6 scripts 332 downloads 11 exports 91 dependencies

Last updated from:013af48c13. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING218
linux-devel-x86_64NOTE339
source / vignettesOK351
linux-release-x86_64NOTE379
macos-release-arm64NOTE226
macos-oldrel-arm64NOTE215
windows-develNOTE281
windows-releaseNOTE261
windows-oldrelNOTE248
wasm-releaseOK167

Exports:forceReverseinitialOrdermethyl_average_statusmethyl_percent_sitesmethyl_proportionmethylscaperplotSequenceprepSCrefineFunctionrunAlignsubsetSC

Dependencies:abindade4base64encBHBiobaseBiocGenericsBiocParallelBiostringsbslibcacachemcliclustercodetoolscolorspacecommonmarkcpp11crayondata.tableDelayedArraydigestfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomicRangesgluehtmltoolshttpuvIRangesiteratorsjquerylibjsonlitelambda.rlaterlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeotelpermutepillarpixmappkgconfigpromisespwalignqapR6rappdirsRcppRcppArmadilloRcppParallelregistryRfastrlangS4ArraysS4VectorssasssegmentedSeqinfoseqinrseriationshinyshinyFilesshinyjssnowsourcetoolsspSparseArraySummarizedExperimenttibbleTSPutf8vctrsveganwithrxtableXVectorzigg

Using methylscaper to visualize joint methylation and nucleosome occupancy data

Rhonda Bacher, Parker Knight

Rendered frommethylScaper.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2024-10-02
Started: 2020-02-06