knowYourCG
This is the released version of knowYourCG; for the devel version, see knowYourCG.
Functional analysis of DNA methylome datasets
Bioconductor version: Release (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]
, Fu Hongxiang [ctb], 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")
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 |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, Epigenetics, MethylationArray, Software |
| Version | 1.2.5 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr |
| 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_1.2.5.tar.gz |
| Windows Binary (x86_64) | knowYourCG_1.2.5.zip |
| macOS Binary (x86_64) | knowYourCG_1.2.5.tgz |
| macOS Binary (arm64) | knowYourCG_1.2.5.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 |
| Old Source Packages for BioC 3.20 | Source Archive |