Package: methylscaper 1.15.0

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]

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methylscaper.pdf |methylscaper.html✨
methylscaper/json (API)

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

Peer review:

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-1.13.3(bioc 3.20)methylscaper-1.12.3(bioc 3.19)

dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning

5.20 score 2 stars 3 scripts 180 downloads 11 exports 99 dependencies

Last updated 23 days agofrom:271ec9148a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTESep 24 2024
R-4.3-macNOTESep 24 2024

Exports:forceReverseinitialOrdermethyl_average_statusmethyl_percent_sitesmethyl_proportionmethylscaperplotSequenceprepSCrefineFunctionrunAlignsubsetSC

Dependencies:abindade4askpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbslibcacachemcliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDelayedArraydigestfansifastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehtmltoolshttpuvhttrIRangesiteratorsjquerylibjsonlitelambda.rlaterlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpermutepillarpixmappkgconfigpromisespwalignqapR6rappdirsRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratregistryRfastrlangS4ArraysS4VectorssasssegmentedseqinrseriationshinyshinyFilesshinyjssnowsourcetoolsspSparseArraySummarizedExperimentsystibbleTSPUCSC.utilsutf8vctrsveganwithrxtableXVectorzlibbioc

Using methylscaper to visualize joint methylation and nucleosome occupancy data

Rhonda Bacher, Parker Knight

Rendered frommethylScaper.Rmdusingknitr::rmarkdownon Oct 30 2024.

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