HiBED

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HiBED.

HiBED

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, PackageTypeData, Tissue

Version 1.2.0

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.

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_1.2.0.tar.gz

Windows Binary (x86_64)

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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