Package: epigraHMM
Title: Epigenomic R-based analysis with hidden Markov models
Version: 1.19.1
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,
        bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5,
        Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap,
        grDevices
LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib
RoxygenNote: 7.3.3
Encoding: UTF-8
SystemRequirements: GNU make
Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle,
        BSgenome.Hsapiens.UCSC.hg19, gcapc, genomationData
VignetteBuilder: knitr
LazyData: true
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: 2026-04-07 23:12:18 UTC
RemoteUrl: https://github.com/bioc/epigraHMM
RemoteRef: HEAD
RemoteSha: 256400ba6daf9f593812f932bdf4a860143f3269
NeedsCompilation: yes
Packaged: 2026-04-08 06:39:04 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-w64-mingw32; 2026-04-08 06:44:46 UTC; windows
Archs: x64
