HiBED

HiBED


Bioconductor version: Release (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

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.
See More
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
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