RnBeads
max planck institut
informatik
mpii logo Minerva of the Max Planck Society
 

RnBeads

Web Service

The basic functionality of RnBeads is available as a web service. This allows small analyses to be performed online, without the need of R installation. Upon successful completion of the pipeline, you will receive an email with the link to the generated reports.

Dataset

To use the RnBeads web service, please prepare a ZIP file that contains the DNA methylation data for all samples that should be included in the analysis. Furthermore, a sample annotation table is required, which should contain relevant information for each sample (such as cell type or disease) and is used by RnBeads to decide which statistical comparisons should be performed.

  • For Infinium 450k assay, the ZIP archive should contain the raw data as two IDAT files per sample, corresponding the red and green channel intensities of the microarray. Importantly, please retain the original names of the IDAT files as they are provided by the Illumina software or Infinium core facility. The sample annotation table should also retain the general form of the table in CSV format provided by the Illumina software or Infinium core facility. It may be amended with additional columns containing those sample annotations that are directly relevant for the analysis.
  • For other DNA methylation assays, the ZIP archive should contain one BED file per sample, which stores absolute DNA methylation levels of each covered cytosine in that sample. Depending on the specific assay used, different methods may be necessary to preprocess the data accordingly. The sample annotation table should contain a column with filenames (referring to the uploaded BED file of each sample) and any additional annotations that are directly relevant for the analysis.

For performance reasons, the RnBeads web service currently accepts only datasets with up to 24 samples, and the size of the ZIP file cannot exceed 200MB. Furthermore, the ZIP archive should only contain the IDAT or BED files, no directories. The sample annotation table should be provided as a CSV file, which can be created using any spreadsheet software. Every row in this table corresponds to one sample from the dataset, and every column denotes a phenotypic or technical property of the samples (e.g., disease status or sample processing date). Example data can be downloaded from here.

ZIP archive of data files
Sample annotation table in CSV format
Email
CAPTCHA  * Please retype the characters shown on the left

Analysis profile

In order to simplify the submission, we have provided three default analysis profiles - one for an Infinium dataset, and two for a bisulfite sequencing dataset. Selecting one of these profiles automatically sets the options in the next section.

Profile

Analysis options

You can customize the analysis pipeline by adjusting the options listed in the table below. Pointing to an option name displays a short description of the functionality. A more detailed explanation of the analysis pipeline is available in the vignette of the R package.

Genome assembly
Style of BED files
Heatmap of SNP probes
Methylation context
Filter out sex chromosomes
Allowed fraction of missing values
Filter out high p-values
Number of principal components
Number of permutations in the correlation test
Beta value distributions
Intersample variability
Clustering based on
GO-enrichment analysis

Submit for analysis

When you press the Submit button below, the specified files will be uploaded and the RnBeads pipeline will be scheduled to run on our server. Uploading might take a few minutes or more depending on your Internet connection and the size of the dataset. Please do not close the browser window before you see the confirmation page.

ZIP archive containing IDAT or BED files and no subdirectories. Sample annotation table in a comma-separated value (CSV) format. Email address to receive a link with the generated reports. Genome assembly to be used; important for bisulfite mode. Format of the BED files containing methylation calls of a bisulfite sequencing data.
Supported formats include Bismark, BisSNP and EPP.
If a heatmap of the intensities of SNP probes for all samples
should be created in the quality control module.
List of probe context types to be included in the analysis. In addition to cytosine methylation,
the Infinium assay contains probes dedicated to SNP detection.
If sites located on sex chromosomes should be removed in the filtering module. Number between 0 and 1, indicating the fraction of allowed missing values per site.
A site is filtered out when its methylation beta values are NAs in a larger
fraction of samples than this threshold. Setting this option to 1 retains all sites;
setting it to 0 causes all sites that contain missing values to be filtered out.
If selected, probes and/or samples with unreliable detection p-values are
removed using an iterative procedure named Greedycut.
Maximum number of principal components to be tested for associations with other factors,
such as sample traits and control probe states.
Number of permutations in tests performed to check for correlation between traits.
A value of 0 disables permutation tests.
Compute and plot beta value distributions for sample groups and site categories. Compute and plot methylation variability in sample groups. Sites to be used when executing and comparing clustering algorithms. Perform Gene Ontology (GO)-enrichment analysis
on the identified differentially methylated regions.