hummingbird
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see hummingbird.
Bayesian Hidden Markov Model for the detection of differentially methylated regions
Bioconductor version: 3.19
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("hummingbird")):
Installation
To install this package, start R (version "4.4") 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")| hummingbird | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, BiomedicalInformatics, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, HiddenMarkovModel, Sequencing, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.0) |
| Imports | Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp |
| 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 | hummingbird_1.14.0.tar.gz |
| Windows Binary (x86_64) | hummingbird_1.14.0.zip |
| macOS Binary (x86_64) | hummingbird_1.14.0.tgz |
| macOS Binary (arm64) | hummingbird_1.14.0.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 |