deconvR
This is the development version of deconvR; for the stable release version, see deconvR.
Simulation and Deconvolution of Omic Profiles
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Irem B. Gündüz <irembgunduz at gmail.com>
citation("deconvR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("deconvR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DNAMethylation, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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, granulator, 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/deconvR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/deconvR |
| Package Short Url | https://bioconductor.org/packages/deconvR/ |
| Package Downloads Report | Download Stats |