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HiBED

HiBED


Bioconductor version: Release (3.18)

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.

Author: Ze Zhang [cre, aut] , Lucas A. Salas [aut]

Maintainer: Ze Zhang <ze.zhang.gr at dartmouth.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HiBED")

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("HiBED")
HiBED HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, PackageTypeData, Tissue
Version 1.0.0
License GPL-3
Depends R (>= 3.5.0)
Imports dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k, minfi, utils, AnnotationHub, SummarizedExperiment
System Requirements
URL https://github.com/SalasLab/HiBED
Bug Reports https://github.com/SalasLab/HiBED/issues.
See More
Suggests knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest
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Package Archives

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

Source Package HiBED_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiBED
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiBED
Package Short Url https://bioconductor.org/packages/HiBED/
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