decemedip
This is the released version of decemedip; for the devel version, see decemedip.
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, Software, WholeGenome |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | decemedip_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | decemedip_1.0.0.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 |