knowYourCG

This is the development version of knowYourCG; for the stable release version, see knowYourCG.

Functional analysis of DNA methylome datasets


Bioconductor version: Development (3.21)

knowYourCG automates the functional analysis of DNA methylation data. The package tests the enrichment of discrete CpG probes across thousands of curated biological and technical features. GSEA-like analysis can be performed on continuous methylation data query sets. knowYourCG can also take beta matrices as input to perform feature aggregation over the curated database sets.

Author: Zhou Wanding [aut], Goldberg David [aut, cre] (ORCID: ), Fu Hongxiang [ctb], Moyer Ethan [ctb]

Maintainer: Goldberg David <golddc72 at pennmedicine.upenn.edu>

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")

# 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("knowYourCG")
5. knowYourCG HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, Epigenetics, MethylationArray, Software
Version 1.3.0
In Bioconductor since BioC 3.19 (R-4.4) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils
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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package knowYourCG_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/knowYourCG
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/knowYourCG
Bioc Package Browser https://code.bioconductor.org/browse/knowYourCG/
Package Short Url https://bioconductor.org/packages/knowYourCG/
Package Downloads Report Download Stats