Package: methylscaper 1.13.0

Rhonda Bacher

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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# Install 'methylscaper' in R:

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

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-1.13.0(bioc 3.20)methylscaper-1.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

11 exports 1.08 score 99 dependencies

Last updated 2 months agofrom:9bdf1c7353

Exports:forceReverse initialOrder methyl_average_status methyl_percent_sites methyl_proportion methylscaper plotSequence prepSC refineFunction runAlign subsetSC

Dependencies:abind ade4 askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bslib ca cachem cli cluster codetools colorspace commonmark cpp11 crayon curl data.table DelayedArray digest fansi fastmap fontawesome foreach formatR fs futile.logger futile.options gclus GenomeInfoDb GenomeInfoDbData GenomicRanges glue htmltools httpuv httr IRanges iterators jquerylib jsonlite lambda.r later lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl permute pillar pixmap pkgconfig promises pwalign qap R6 rappdirs Rcpp RcppArmadillo RcppGSL RcppParallel RcppZiggurat registry Rfast rlang S4Arrays S4Vectors sass segmented seqinr seriation shiny shinyFiles shinyjs snow sourcetools sp SparseArray SummarizedExperiment sys tibble TSP UCSC.utils utf8 vctrs vegan withr xtable XVector zlibbioc

Using methylscaper to visualize joint methylation and nucleosome occupancy data

Rhonda Bacher, Parker Knight

Rendered frommethylScaper.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2021-05-24
Started: 2020-02-06

Help page	Topics
Check if a package is installed	check_package
Force reversal of a subset of the ordering	forceReverse
Human gene symbols and positions	human_bm
Ordering the molecules/reads	initialOrder
Calculate the average methylation/accessibility status across all cells/molecules.	methyl_average_status
Calculates the percentage of methylated cells/molecules per site	methyl_percent_sites
Calculate the proportion of methylated bases for each cell/molecule	methyl_proportion
methylscaper	methylscaper
Mouse gene symbols and positions	mouse_bm
Generate Sequence Plot	plotSequence
Process single-cell data	prepSC
Example reads from single-molecule experiment	reads_sm
Example reference sequence to align reads to from a single-molecule experiment	ref_seq
Refinement	refineFunction
This is an internal function for now and a place-holder in case SingleCellExperiment may be used in the future. We may need to update this later. Assumes rownames are formatted like chr_pos and there are two assays. The assay names are `methylation_met` for endogenous methylation and `methylation_acc` for accessibility.	reformatSCE
Align the single-molecule data	runAlign
Example preprocessed single-cell experiment subset	singlecell_subset
Example preprocessed single-molecule experiment	singlemolecule_example
Load in methylation data	subsetSC

Package: methylscaper 1.13.0

methylscaper: Visualization of Methylation Data

Using methylscaper to visualize joint methylation and nucleosome occupancy data

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Readme and manuals

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Usage by other packages (reverse dependencies)