decemedip
This is the development version of decemedip; for the stable release version, see decemedip.
All Bioconductor versions of decemedip
3.24 (devel), 3.23 (release)
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome
Bioconductor version: 3.24 · Package version: 1.1.3
The R package decemedip is a novel computational paradigm developed for inferring the relative abundances of cell types and tissues measure by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). This paradigm allows using reference data from other technologies such as microarray or WGBS.
Author: Keegan Korthauer [aut, cre] 
, Ning Shen [aut]
Maintainer: Keegan Korthauer <kkorthauer at cmmt.ubc.ca>
Citation
From within R, enter citation("decemedip"):
Keegan Korthauer, Ning Shen. decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome. doi:10.18129/B9.bioc.decemedip, R package version 1.1.3, https://bioconductor.org/packages/decemedip.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("decemedip")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.3 |
| License | MIT + file LICENSE |
| URL | https://github.com/nshen7/decemedip |
| Bug Reports | https://github.com/nshen7/decemedip/issues |
| System Requirements | GNU make |
| Last updated | 2026-09-23 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2262 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/decemedip/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("decemedip")| Cell type deconvolutiond of (cf)MeDIP-seq data with decemedip | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | decemedip_1.1.3.tar.gz |
| Windows binary (x86_64) | decemedip_1.1.3.zip |
| macOS binary (arm64) | decemedip_1.1.3.tgz |
| macOS binary (x86_64) | decemedip_1.1.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/decemedip |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/decemedip |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: bayesplot, cowplot, dplyr, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, matrixStats, MEDIPS, methods, purrr, R.utils, Rcpp, RcppParallel, rlang, rstan, rstantools, S4Vectors, SummarizedExperiment
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0)