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This is the development version of dinoR; for the stable release version, see dinoR.

Differential NOMe-seq analysis

Bioconductor version: Development (3.20)

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.

Author: Michaela Schwaiger [aut, cre]

Maintainer: Michaela Schwaiger <michaela.schwaiger at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

dinoR-vignette HTML R Script
Reference Manual PDF


biocViews Coverage, DifferentialMethylation, Epigenetics, MethylSeq, NucleosomePositioning, Sequencing, Software, Transcription
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0), SummarizedExperiment
Imports BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package dinoR_1.1.0.tar.gz
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macOS Binary (arm64) dinoR_1.1.0.tgz
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