dinoR
This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see dinoR.
Differential NOMe-seq analysis
Bioconductor version: 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 fmi.ch>
citation("dinoR")):
Installation
To install this package, start R (version "4.4") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dinoR")| dinoR-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DifferentialMethylation, Epigenetics, MethylSeq, NucleosomePositioning, Sequencing, Software, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1 year) |
| 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 |
| System Requirements | |
| URL | https://github.com/xxxmichixxx/dinoR |
| Bug Reports | https://github.com/xxxmichixxx/dinoR/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dinoR_1.2.0.tar.gz |
| Windows Binary (x86_64) | dinoR_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | dinoR_1.2.0.tgz |
| macOS Binary (arm64) | dinoR_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dinoR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dinoR |
| Bioc Package Browser | https://code.bioconductor.org/browse/dinoR/ |
| Package Short Url | https://bioconductor.org/packages/dinoR/ |
| Package Downloads Report | Download Stats |