decemedip
This is the development version of decemedip; to use it, please install the devel version of Bioconductor.
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome
Bioconductor version: Development (3.23)
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.
Maintainer: Ning Shen <ning.shen.wk at gmail.com>
citation("decemedip")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("decemedip")
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("decemedip")| Cell type deconvolutiond of (cf)MeDIP-seq data with decemedip | HTML | R Script |
| Reference Manual |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, Software, WholeGenome |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | GNU make |
| URL | https://github.com/nshen7/decemedip |
| Bug Reports | https://github.com/nshen7/decemedip/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0) |
| Linking To | 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) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | decemedip_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | decemedip_0.99.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/decemedip |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/decemedip |
| Bioc Package Browser | https://code.bioconductor.org/browse/decemedip/ |
| Package Short Url | https://bioconductor.org/packages/decemedip/ |
| Package Downloads Report | Download Stats |