Package: dinoR
Title: Differential NOMe-seq analysis
Version: 1.4.0
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
git_url: https://git.bioconductor.org/packages/dinoR
git_branch: RELEASE_3_21
git_last_commit: 60ff23b
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:15:53 UTC; biocbuild
Author: Michaela Schwaiger [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4522-7810>)
Maintainer: Michaela Schwaiger <michaela.schwaiger@fmi.ch>
Built: R 4.5.0; ; 2025-04-16 14:20:10 UTC; windows
