Package: hummingbird
Type: Package
Title: Bayesian Hidden Markov Model for the detection of differentially
        methylated regions
Version: 1.20.0
Authors@R: c(person("Eleni", "Adam", email = "eadam002@odu.edu", role = c("aut", "cre")), person("Tieming", "Ji", role = c("aut")), person("Desh", "Ranjan", role = c("aut")))
Description: 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.
License: GPL (>=2)
Depends: R (>= 4.0)
Encoding: UTF-8
LazyData: true
Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
Suggests: knitr, rmarkdown, BiocStyle
LinkingTo: Rcpp
biocViews: HiddenMarkovModel, Bayesian, DNAMethylation,
        BiomedicalInformatics, Sequencing, GeneExpression,
        DifferentialExpression, DifferentialMethylation
VignetteBuilder: knitr
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:01:14 UTC
RemoteUrl: https://github.com/bioc/hummingbird
RemoteRef: RELEASE_3_22
RemoteSha: 88acb8584b088997d8f635bb7b1fc4119fed3d4e
NeedsCompilation: yes
Packaged: 2025-11-16 07:37:29 UTC; root
Author: Eleni Adam [aut, cre],
  Tieming Ji [aut],
  Desh Ranjan [aut]
Maintainer: Eleni Adam <eadam002@odu.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-16 07:39:02 UTC; windows
Archs: x64
