deconvR
This is thereleased version of deconvR; for the devel version, seedeconvR.
Simulation and Deconvolution of Omic Profiles
Bioconductor version: Release (3.22)
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: 0000-0003-2641-0916, Veronika Ebenal [aut] ORCID: 0000-0001-7976-3964, Altuna Akalin [aut] ORCID: 0000-0002-0468-0117
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")BiocManager::install("deconvR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.16.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 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
FollowInstallation instructions to use this package in your R session.
| Source Package | deconvR_1.16.0.tar.gz |
| Windows Binary (x86_64) | deconvR_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | deconvR_1.16.0.tgz |
| macOS Binary (arm64) | deconvR_1.16.0.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 |