Package: scmeth 1.25.0

Divy Kangeyan

scmeth: Functions to conduct quality control analysis in methylation data

Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

Authors:Divy Kangeyan <[email protected]>

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NEWS

# Install 'scmeth' in R:

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

Bug tracker:https://github.com/aryeelab/scmeth/issues

On BioConductor:scmeth-1.25.0(bioc 3.20)scmeth-1.24.0(bioc 3.19)

bioconductor-package

12 exports 1.00 score 152 dependencies 1 mentions

Last updated 2 months agofrom:363cbc55bb

Exports:bsConversionPlot chromosomeCoverage coverage cpgDensity cpgDiscretization downsample featureCoverage mbiasplot methylationDist readmetrics repMask report

Dependencies:abind AnnotationDbi AnnotationHub annotatr askpass base64enc beachmat BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome bslib bsseq cachem cli clipr codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dplyr DT evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable gtools HDF5Array highr hms htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl permute pillar pkgconfig plogr plyr png prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr regioneR reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML XVector yaml zlibbioc

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Readme and manuals

Help Manual

Help page	Topics
Bisulfite conversion rate visualization	bsConversionPlot
CpG covergae in each chromosome	chromosomeCoverage
Coverage for single cells	coverage
Provides Coverage by the CpG density. CpG Density is defined as the number of CpGs observed in certain base pair long region.	cpgDensity
Discretize the CpG methylation values to align with single cell analysis	cpgDiscretization
Downsample analysis	downsample
Coverage based on the genomic feature	featureCoverage
Methylation bias plot	mbiasplot
Provide graphics for methylation distribution	methylationDist
Provide graphics for read information	readmetrics
Provides Coverage metrics in the repeat masker region	repMask
Generates an inclusive report on methylation analysis	report
scmeth: a package to conduct quality control analysis for methylation data. Most functions can be applied to both bulk and single-cell methylation while other functions are specific to single-cell methylation data. scmeth is especially customized to use the output from the FireCloud implementation of methylation pipeline to produce comprehensive quality control report	scmeth-package scmeth