deconvR

DOI: 10.18129/B9.bioc.deconvR    

This is the development version of deconvR; for the stable release version, see deconvR.

Simulation and Deconvolution of Omic Profiles

Bioconductor version: Development (3.15)

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: İrem B. Gündüz [aut, cre] , Veronika Ebenal [aut] , Altuna Akalin [aut]

Maintainer: İrem B. Gündüz <irembgunduz at gmail.com>

Citation (from within R, enter citation("deconvR")):

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("deconvR")

 

HTML R Script deconvRVignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
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
SystemRequirements
Enhances
URL https://github.com/BIMSBbioinfo/deconvR
BugReports https://support.bioconductor.org/t/deconvR
Depends On Me
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package deconvR_1.1.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) deconvR_1.1.1.tgz
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/
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