Package: epigraHMM
Title: Epigenomic R-based analysis with hidden Markov models
Version: 1.21.2
Date: 2025-09-16
Authors@R: c(person("Pedro", "Baldoni", email = "pedrobaldoni@gmail.com", role = c("aut","cre")))
biocViews: ChIPSeq, ATACSeq, DNaseSeq, HiddenMarkovModel, Epigenetics
Description: 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.
License: MIT + file LICENSE
Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods,
        Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools, csaw,
        S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales,
        ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices
LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib
Encoding: UTF-8
SystemRequirements: GNU make
Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle,
        BSgenome.Hsapiens.UCSC.hg19, gcapc, genomationData
VignetteBuilder: knitr
LazyData: true
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-12 23:38:42 UTC
RemoteUrl: https://github.com/bioc/epigraHMM
RemoteRef: HEAD
RemoteSha: 17ec9bb8e25b7566427d107100e9ad6da05add40
NeedsCompilation: yes
Packaged: 2026-06-12 11:07:50 UTC; root
Author: Pedro Baldoni [aut, cre]
Maintainer: Pedro Baldoni <pedrobaldoni@gmail.com>
Depends: R (>= 3.5.0)
Built: R 4.6.0; x86_64-apple-darwin20; 2026-06-12 11:14:58 UTC; unix
