This is the released version of dinoR; for the devel version, see dinoR.
Differential NOMe-seq analysisBioconductor version: Release (3.21)
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] ORCID: 0000-0002-4522-7810
Maintainer: Michaela Schwaiger <michaela.schwaiger at fmi.ch>
Citation (from within R, entercitation("dinoR")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dinoR")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dinoR")Follow Installation instructions to use this package in your R session.
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