Bioconductor - knowYourCG

Bioconductor - knowYourCG
Bioconductor 3.22
Software Packages
knowYourCG
knowYourCG
This is the
released
version of knowYourCG; for the devel version, see
knowYourCG
Functional analysis of DNA methylome datasets
DOI:
10.18129/B9.bioc.knowYourCG
Bioconductor version:
Release (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, fnd]
ORCID: 0000-0001-9126-1932
, Goldberg David [aut, cre]
ORCID: 0000-0002-9622-4708
, Fu Hongxiang [ctb]
Maintainer:
Goldberg David
Citation (from within R, enter
citation("knowYourCG")
):
Installation
To install this package, start R (version "4.5") 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")
1. Sequencing Data Analysis
HTML
R Script
2. Array Data Analysis
HTML
R Script
3. Continuous Variable Enrichment Analysis
HTML
R Script
4. Enrichment Visualization
HTML
R Script
Reference Manual
PDF
NEWS
Text
LICENSE
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
DNAMethylation
Epigenetics
MethylationArray
Sequencing
SingleCell
Software
Spatial
Transcription
Version
1.6.3
In Bioconductor since
BioC 3.19 (R-4.4) (2 years)
License
MIT + file
LICENSE
Depends
R (>= 4.4.0)
Imports
sesameData
ExperimentHub
AnnotationHub
dplyr
, methods,
rlang
GenomicRanges
IRanges
reshape2
S4Vectors
, stats,
stringr
, utils,
ggplot2
ggrepel
tibble
wheatmap
magrittr
System Requirements
URL
Bug Reports
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
Package Archives
Follow
Installation
instructions to use this package in your R session.
Source Package
knowYourCG_1.6.3.tar.gz
Windows Binary (x86_64)
knowYourCG_1.5.2.zip
macOS Binary (x86_64)
knowYourCG_1.6.0.tgz
macOS Binary (arm64)
knowYourCG_1.6.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/knowYourCG
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/knowYourCG
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