hummingbird
This is the development version of hummingbird; for the stable release version, see hummingbird.
All Bioconductor versions of hummingbird
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12
Bayesian Hidden Markov Model for the detection of differentially methylated regions
Bioconductor version: 3.24 · Package version: 1.23.0
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>
Citation
From within R, enter citation("hummingbird"):
Eleni Adam, Tieming Ji, Desh Ranjan. hummingbird: Bayesian Hidden Markov Model for the detection of differentially methylated regions. doi:10.18129/B9.bioc.hummingbird, R package version 1.23.0, https://bioconductor.org/packages/hummingbird.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("hummingbird")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.23.0 |
| License | GPL (>=2) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| Downloads rank | 1685 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, BiomedicalInformatics, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, HiddenMarkovModel, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/hummingbird/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("hummingbird")| The hummingbird | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | hummingbird_1.23.0.tar.gz |
| Windows binary (x86_64) | hummingbird_1.23.0.zip |
| macOS binary (arm64) | hummingbird_1.23.0.tgz |
| macOS binary (x86_64) | hummingbird_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hummingbird |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hummingbird |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.0)
Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
LinkingTo: Rcpp