decemedip
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("decemedip")Details
| Maintainer | Ning Shen <ning.shen.wk@gmail.com> |
| Author | Ning Shen [aut, cre] (ORCID: <https://orcid.org/0000-0002-2974-1086>) |
| License | MIT + file LICENSE |
| URL | https://github.com/nshen7/decemedip |
| Bug Reports | https://github.com/nshen7/decemedip/issues |
| System Requirements | GNU make |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/decemedip/ |
Citation
From within R, enter citation("decemedip"):
Ning Shen. decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome. doi:10.18129/B9.bioc.decemedip, R package version 1.0.0, https://bioconductor.org/packages/decemedip.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | decemedip_1.0.0.tar.gz |
| Windows binary (x86_64) | decemedip_1.0.0.zip |
| macOS binary (arm64) | decemedip_1.0.0.tgz |
| macOS binary (x86_64) | decemedip_1.0.0.tgz |
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)