knowYourCG
This is the released version of knowYourCG; for the devel version, see knowYourCG.
Functional analysis of DNA methylome datasets
Bioconductor version: Release (3.23)
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 (<doi:10.1126/sciadv.adw3027>). KnowYourCG v2, a command-line implementation in C, is available at <https://github.com/zhou-lab/kycg>.
Author: Wanding Zhou [aut, fnd] 
, David Goldberg [aut, cre] , Hongxiang Fu [ctb]
Maintainer: David Goldberg <golddc72 at pennmedicine.upenn.edu>
citation("knowYourCG")):Wanding Zhou, David Goldberg. knowYourCG: Functional analysis of DNA methylome datasets. doi:10.18129/B9.bioc.knowYourCG, R package version 1.8.3, https://bioconductor.org/packages/knowYourCG.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("knowYourCG")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("knowYourCG")| "2. Array Data Analysis" | HTML | R Script |
| "3. Continuous Variable Enrichment Analysis" | HTML | R Script |
| "1. Sequencing Data Analysis" | HTML | R Script |
| "4. Enrichment Visualization" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, MethylationArray, Sequencing, SingleCell, Software, Spatial, Transcription |
| Version | 1.8.3 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | sesameData, ExperimentHub, AnnotationHub, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr, readr |
| System Requirements | |
| URL | https://github.com/zhou-lab/knowYourCG |
| Bug Reports | https://github.com/zhou-lab/knowYourCG/issues |
See More
| Suggests | testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2, ggrastr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | knowYourCG_1.8.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | knowYourCG_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | knowYourCG_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/knowYourCG |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/knowYourCG |
| Package Short Url | https://bioconductor.org/packages/knowYourCG/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |