scmeth-package |
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 |
bsConversionPlot |
Bisulfite conversion rate visualization |
chromosomeCoverage |
CpG covergae in each chromosome |
coverage |
Coverage for single cells |
cpgDensity |
Provides Coverage by the CpG density. CpG Density is defined as the number of CpGs observed in certain base pair long region. |
cpgDiscretization |
Discretize the CpG methylation values to align with single cell analysis |
downsample |
Downsample analysis |
featureCoverage |
Coverage based on the genomic feature |
mbiasplot |
Methylation bias plot |
methylationDist |
Provide graphics for methylation distribution |
readmetrics |
Provide graphics for read information |
repMask |
Provides Coverage metrics in the repeat masker region |
report |
Generates an inclusive report on methylation analysis |
scmeth |
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 |