This tutorial introduces RnBeadsDJ, a graphical user interface to configure and run RnBeads analyses
A vignette providing step-by-step instructions on how to run the tutorial is available here.
Download and extract the following file:
Visit the CRAN website and download the version of R corresponding to your platform. Install R using the downloaded executable.
You can find detailed instructions on how to install RnBeads and ghostscript following this link.
Follow the instructions provided in the tutorial vignette.
Reports for the examples discussed in the tutorial are available here:
This tutorial contains instructions and material for the workshop on "Analyzing Methylome Data using RnBeads" that was presented at the Epigenomics 2016 (Puerto Rico) meeting. To get R and RnBeads set up for the tutorial and to retrieve the example data, please follow steps 1, 2 and 3 described below. Afterwards, feel free to experiment with the code contained in the downloaded data directory.
The presentation slides from the workshop are available here.
Download and extract the following file for the tutorial:
If you don't want to download the entire data package at once, you can also download the files individually:
Visit the CRAN website and download the version of R corresponding to your platform. Install R using the downloaded executable.
You can find detailed instructions on how to install RnBeads and ghostscript following this link.
Follow the instructions provided in the presentation.
Reports for the examples discussed in the tutorial are available here:
Here, we provide instructions for how to use the epigenetic age prediction tool MethylAger. MethylAger was created as an RnBeads module and is therefore applicable to all DNA methylation assays operating at single base pair resolution. MethylAger contains several predefined predictors that were extensively evaluated for the most frequently used DNA methylation assays (e.g. 27K, 450K and RRBS). Depending on the type of the input data set, MethylAger decides which of these predictors is applicable. Additionally, a custom predictor can be created from the provided data set. For a detailed description of the methods employed and of the predefined predictors explore this website. Similar to the tutorial described above, an installation of R is needed. Then follow the instructions and enjoy the functions of the epigenetic age prediction tool MethylAger.
The data package, including the R tutorial and an example data set can be downloaded here (233 MB).
Follow the instructions provided in the R tutorial and analyze the example data set to get used to MethylAger.
This brief vignette demonstrates a cross-platform integration of DNA methylation data from Illumina EPIC v1 and EPIC v2 microarrays.
This tutorial is a brief demo of the new functionality for the joint storage and analysis of data from different DNA methylation profiling platforms. The updated combine method enables pair-wise merging of all classes of data containers. Obtained hybrid data sets can be used for any standard RnBeads analysis. The tutorial demonstrates new functionality using pubicly available data of primary prostate cancer samples and cell lines from the EPIC array evaluation study [Pidsley et al., Genome Biology, 2016]
RnBeads relies on annotation packages – one for every supported genome assembly. The ones currently supported are hg19, hg38, mm9, mm10 and rn5. If you would like to analyze a different genome, you need to create a new annotation package. RnBeadsAnnotationCreator facilitates the generation of annotation packages for RnBeads.
A dedicated vignette (download PDF) explains how RnBeads annotation packages are structured and includes a tutorial on creating an annotation package for the Zebrafish genome.