knowYourCG
This is the development version of knowYourCG; for the stable release version, see knowYourCG.
Functional analysis of DNA methylome datasets
Bioconductor version: Development (3.20)
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] , Moyer Ethan [ctb]
Maintainer: Goldberg David <golddc72 at pennmedicine.upenn.edu>
citation("knowYourCG")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | DNAMethylation, Epigenetics, MethylationArray, Software |
Version | 1.1.0 |
In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
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 |
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_1.1.0.tar.gz |
Windows Binary | knowYourCG_1.1.0.zip |
macOS Binary (x86_64) | knowYourCG_1.1.0.tgz |
macOS Binary (arm64) | knowYourCG_1.1.0.tgz |
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 |