Package: hummingbird
Type: Package
Title: Bayesian Hidden Markov Model for the detection of differentially
        methylated regions
Version: 1.2.0
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
LinkingTo: Rcpp
biocViews: HiddenMarkovModel, Bayesian, DNAMethylation,
        BiomedicalInformatics, Sequencing, GeneExpression,
        DifferentialExpression, DifferentialMethylation
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/hummingbird
git_branch: RELEASE_3_13
git_last_commit: 1d22c8a
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: yes
Packaged: 2021-05-20 00:34:49 UTC; biocbuild
Author: Eleni Adam [aut, cre],
  Tieming Ji [aut],
  Desh Ranjan [aut]
Maintainer: Eleni Adam <eadam002@odu.edu>
Built: R 4.1.0; i386-w64-mingw32; 2021-05-20 08:32:06 UTC; windows
Archs: i386, x64
