This is the development version of knowYourCG; for the stable release version, see knowYourCG.
Functional analysis of DNA methylome datasetsBioconductor version: Development (3.22)
KnowYourCG (KYCG) is a supervised learning framework designed for the functional analysis of DNA methylation data. Unlike existing tools that focus on genes or genomic intervals, KnowYourCG directly targets CpG dinucleotides, featuring automated supervised screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait-epigenome associations. KnowYourCG addresses the challenges of data sparsity in various methylation datasets, including low-pass Nanopore sequencing, single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies and epigenetic clocks.
Author: Zhou Wanding [aut] ORCID: 0000-0001-9126-1932 , Goldberg David [aut, cre] ORCID: 0000-0002-9622-4708 , Fu Hongxiang [ctb]
Maintainer: Goldberg David <golddc72 at pennmedicine.upenn.edu>
Citation (from within R, entercitation("knowYourCG")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("knowYourCG")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("knowYourCG")Follow Installation instructions to use this package in your R session.
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