hummingbird

DOI: 10.18129/B9.bioc.hummingbird  

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bioconductor version: Release (3.16)

A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

Author: Eleni Adam [aut, cre], Tieming Ji [aut], Desh Ranjan [aut]

Maintainer: Eleni Adam <eadam002 at odu.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("hummingbird")

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("hummingbird")

 

HTML	R Script	hummingbird
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, BiomedicalInformatics, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, HiddenMarkovModel, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL (>=2)
Depends	R (>= 4.0)
Imports	Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
LinkingTo	Rcpp
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	hummingbird_1.8.0.tar.gz
Windows Binary	hummingbird_1.8.0.zip
macOS Binary (x86_64)	hummingbird_1.8.0.tgz
macOS Binary (arm64)	hummingbird_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/hummingbird
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hummingbird
Bioc Package Browser	https://code.bioconductor.org/browse/hummingbird/
Package Short Url	https://bioconductor.org/packages/hummingbird/
Package Downloads Report	Download Stats