Package: dinoR
Title: Differential NOMe-seq analysis
Version: 1.6.0
Authors@R: 
    person("Michaela", "Schwaiger",, "michaela.schwaiger@fmi.ch", 
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-4522-7810"))
Description: dinoR tests for significant differences in NOMe-seq
        footprints between two conditions, using genomic regions of
        interest (ROI) centered around a landmark, for example a
        transcription factor (TF) motif. This package takes NOMe-seq
        data (GCH methylation/protection) in the form of a Ranged
        Summarized Experiment as input. dinoR can be used to group
        sequencing fragments into 3 or 5 categories representing
        characteristic footprints (TF bound, nculeosome bound, open
        chromatin), plot the percentage of fragments in each category
        in a heatmap, or averaged across different ROI groups, for
        example, containing a common TF motif. It is designed to
        compare footprints between two sample groups, using edgeR's
        quasi-likelihood methods on the total fragment counts per ROI,
        sample, and footprint category.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR,
        GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr,
        tibble, tidyr, tidyselect
Depends: R (>= 4.3.0), SummarizedExperiment
LazyData: false
biocViews: NucleosomePositioning, Epigenetics, MethylSeq,
        DifferentialMethylation, Coverage, Transcription, Sequencing,
        Software
URL: https://github.com/xxxmichixxx/dinoR
BugReports: https://github.com/xxxmichixxx/dinoR/issues
Config/pak/sysreqs: libicu-dev libpng-dev perl
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:28:52 UTC
RemoteUrl: https://github.com/bioc/dinoR
RemoteRef: RELEASE_3_22
RemoteSha: 5d0a090566d7e944ae7fafe8802dc756a55d713f
NeedsCompilation: no
Packaged: 2025-11-11 16:37:22 UTC; root
Author: Michaela Schwaiger [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4522-7810>)
Maintainer: Michaela Schwaiger <michaela.schwaiger@fmi.ch>
Built: R 4.5.2; ; 2025-11-11 16:41:21 UTC; windows
