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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

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/
Package Downloads Report	Download Stats