DOI: 10.18129/B9.bioc.deconvR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see deconvR.

Simulation and Deconvolution of Omic Profiles

Bioconductor version: 3.16

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>

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biocViews DNAMethylation, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics
Version 1.4.3
In Bioconductor since BioC 3.14 (R-4.1) (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
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
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