RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution. Supported assays include Infinium 450K microarray and bisulfite sequencing protocols, and also MeDIP-seq and MBD-seq once the data have been preprocessed with DNA methylation level inference software. RnBeads implements an analysis workflow that is significantly more comprehensive than those of existing tools. It documents its results in a highly annotated and readable hypertext report, and it scales to the large sample sizes that are becoming the norm for DNA methylation analysis in human cohorts.
NOTE: If you have suggestions for improving RnBeads or if you run into technical problems, please feel free to contact us at firstname.lastname@example.org - ideally with a detailed description and test case illustrating your point.
- 2014-09-28: A paper describing RnBeads has been published.
- 2014-09-20: RnBeads version 0.99.16 has been released. Updates include improved performance when loading sequencing data, default storage of large objects to disk (rather than in main memory), better inference of cell type heterogeneity, new features for paired-samples analysis and simplified parallelization of RnBeads analysis on a scientific computing cluster.
- 2014-09-19: It's "Talk like a pirate day". And what's a pirate's favorite programming language? - Rrrrrrrrrrr!
- 2014-08-08: RnBeads version 0.99.15 has been released. The module structure has been revised. See the news file, the figure below and the FAQ page for specific name changes in the modules and options.
- 2014-04-19: RnBeads version 0.99.13 has been released. New features include batch effects correction using surrogate variable analysis, correction for cell type composition, gender prediction, and many more.
- 2014-02-21: RnBeads version 0.99.12 has been released. Bismark coverage files are now supported as an input and the loading interface has been improved.
- 2014-01-27: RnBeads version 0.99.11 has been released. This version introduces major performance improvements. Also, RnBeads now calculates limma-based p-values in the differential methylation, which also enables correction for known confounders as well as paired sample analysis. For bisulfite sequencing data, RnBeads now supports four genomes - human (hg19), two versions of the mouse genome (mm10, mm9), and rat (rn5). Support for the Infinium 27k assay has also been added.
- 2013-11-06: RnBeads version 0.99.10 has been released. Performance was greatly improved and big data matrices can be stored on the hard disk rather than in main memory now. Furthermore, filtering was divided up into two parts: one before and one after normalization. New normalization methods like the ones from wateRmelon were also added. Some of the plots have a new look.
- 2013-06-17: RnBeads version 0.99.9 has been released. New features include paired sample analysis and improved data loading.
- 2013-05-10: RnBeads version 0.99.7 has been released. New features include background subtraction and BMIQ normalization of Infinium 450k data, as well as differential methylation analysis on all pairs of sample groups.
- 2013-04-14: RnBeads version 0.99.6 has been released. New features include support for bisulfite sequencing (for human and mouse genomes), data export, locus profiling, multicore processing, and various other improvements.
To install RnBeads, please follow the installation instructions on the download page or in the package vignette.
The figure below illustrates the general workflow of RnBeads. The full documentation is available in the package vignette and the reference manual.
Various DNA methylation assays and input formats are supported. The pipeline implements state-of-the-art normalization techniques. Experimental quality control can be conducted and sample outliers and mix-ups can be identified. The package provides flexible methods for CpG and sample filtering. According to sample annotations, batch effects and phenotype covariates can be identified. DNA methylation distributions are analyzed and intergroup as well as intragroup variability in methylation profiles is quantified. Furthermore, differential methylation between groups of samples can be characterized. The analysis is based on individual CpGs as well as on predefined or custom genomic regions. Finally, methylation data can be exported in various formats including genome browser views. Comprehensive, highly interpretable reports containing method descriptions, publication grade plots and data tables are generated. Their HTML format facilitates easy tracking and comparison of analyses as well as exchanging results with collaboration partners. Due to its modularized concept, both first-time users and experts can conveniently perform analyses according to their individual demands. A single, comprehensive analysis run can be invoked by specifying only few parameters and executing a master command. Alternatively, a user may execute the steps of the pipeline individually.
RnBeads is available as an open source R package. We encourage user feedback and contributions. If you have any feature requests or want to use or contribute to the RnBeads source code, please contact us at email@example.com and we will be happy to assist you.