deconvR
This is the development version of deconvR; for the stable release version, see deconvR.
Simulation and Deconvolution of Omic Profiles
Bioconductor version: Development (3.24)
This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
Author: Irem B. Gündüz [aut, cre]
, Veronika Ebenal [aut]
, Altuna Akalin [aut]
Maintainer: Irem B. Gündüz <irembgunduz at gmail.com>
citation("deconvR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("deconvR")
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("deconvR")| deconvRVignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics |
| Version | 1.19.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), data.table (>= 1.14.0) |
| Imports | S4Vectors(>= 0.30.0), methylKit(>= 1.18.0), IRanges(>= 2.26.0), GenomicRanges(>= 1.44.0), BiocGenerics(>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi |
| System Requirements | |
| URL | https://github.com/BIMSBbioinfo/deconvR |
| Bug Reports | https://support.bioconductor.org/t/deconvR |
See More
| Suggests | testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle(>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, RefManageR |
| 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 | deconvR_1.19.1.tar.gz |
| Windows Binary (x86_64) | deconvR_1.19.1.zip |
| macOS Binary (big-sur-x86_64) | deconvR_1.19.1.tgz |
| macOS Binary (sonoma-arm64) | deconvR_1.19.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/deconvR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/deconvR |
| Bioc Package Browser | https://code.bioconductor.org/browse/deconvR/ |
| Package Short Url | https://bioconductor.org/packages/deconvR/ |
| Package Downloads Report | Download Stats |