dinoR
This is the development version of dinoR; for the stable release version, see dinoR.
Differential NOMe-seq analysis
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | dinoR_1.9.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | dinoR_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | dinoR_1.9.0.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 |