epigraHMM

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see epigraHMM.

Epigenomic R-based analysis with hidden Markov models

Bioconductor version: 3.15

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

Author: Pedro Baldoni [aut, cre]

Maintainer: Pedro Baldoni <pedrobaldoni at gmail.com>

Citation (from within R, enter citation("epigraHMM")):

Installation

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


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

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("epigraHMM")

Consensus and Differential Peak Calling With epigraHMM HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, HiddenMarkovModel, Software

Version 1.4.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

License MIT + file LICENSE

Depends R (>= 3.5.0)

Imports Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices

System Requirements GNU make

URL

Suggests testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData

Linking To Rcpp, RcppArmadillo, Rhdf5lib

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 epigraHMM_1.4.0.tar.gz

Windows Binary epigraHMM_1.4.0.zip

macOS Binary (x86_64) epigraHMM_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/epigraHMM

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epigraHMM

Bioc Package Browser https://code.bioconductor.org/browse/epigraHMM/

Package Short Url https://bioconductor.org/packages/epigraHMM/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.15 Source Archive