RnBeads protocols

View RnBeads computational protocol

RnBeads statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Bioinformatics workflows Background correction Data analysis Differentially methylated region detection Raw data import Probe filtering Cell composition correction Batch effect correction Normalization Differential methylation site detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

RnBeads specifications

Information


Unique identifier OMICS_00800
Name RnBeads
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Publication for RnBeads

RnBeads in pipelines

 (7)
2017
PMCID: 5478666
PMID: 28634372
DOI: 10.1038/s41598-017-03682-0

[…] with lumi r package. all differential methylation analyses were adjusted for age due to the effect it has on methylation levels., for single cpg level differential methylation analysis, we used rnbeads, seqlm, and since we detected a slightly abnormal distribution in our data, also wilcoxon signed-rank test. false discovery rate (fdr) adjusted p-value < 0.05 was considered […]

2017
PMCID: 5559542
PMID: 28814741
DOI: 10.1038/s41598-017-08595-6

[…] family included in the same experiment. for each experiment, quality control and data pre-processing were performed separately, while the same analytic tools and methods were applied. the r package rnbeads was applied to extract methylation values. in the quality control, a series of probe and sample filtering steps were followed: probes mapping to sex chromosomes, associated with snps and/or […]

2017
PMCID: 5736667
PMID: 29259247
DOI: 10.1038/s41467-017-02177-w

[…] methylation analysis between sample groups (i.e., hscs vs. committed blood cell populations and between jmml sample groups) was performed using the rnb.run.differential function from the rnbeads package. probes with false discovery rate-corrected p-value < 0.05 and a methylation difference (δmeth) ≥ 0.2 were considered as dmps. all analyses were carried out in an r computing […]

2016
PMCID: 5302953
PMID: 27462864
DOI: 10.18632/oncotarget.10792

[…] the beta-mixture quantile normalization (bmiq) []. furthermore, we downloaded dna methylation data with clinical data of hcc from the cancer genome atlas (tcga). data processing was performed using rnbeads software. we thus use the same background correction-method with genomestudio software and bmiq method were used for the normalization process. after excluding aberrant samples by probe […]

2015
PMCID: 4304832
PMID: 25233806
DOI: 10.1016/j.ymeth.2014.08.011

[…] developed a statistical method using reference data to accurately estimate relative proportions of differing cell types in whole blood. this method has been incorporated into methods in minfi and rnbeads. guintivano et al. have implemented a similar method for particular brain cell types. a reference dataset for each cell type would be the ideal solution and the international human epigenome […]


To access a full list of citations, you will need to upgrade to our premium service.

RnBeads in publications

 (76)
PMCID: 5923294
PMID: 29703973
DOI: 10.1038/s41598-018-25085-5

[…] and expression analysis core facility (bea), karolinska institutet, sweden. the array data were preprocessed and then processed using r statistical programme language version 3.1.2 using rnbeads (http://rnbeads.mpi-inf.mpg.de/). analysis with rnbeads included the following steps: (1) loading raw intensity data (idat); (2) prefiltering (removal of snp-enriched probes, greedycut […]

PMCID: 5945969
PMID: 29761124
DOI: 10.1002/acn3.560

[…] gene expression., dna was extracted from peripheral blood using standard methods. dna methylation was quantified using the illumina human methylation 450k microarray. preprocessing was run with the rnbeads package, using the default options for quality control. background correction was performed with the normal exponential convolution, using out‐of‐band probes (noob) method, and arrays […]

PMCID: 5875016
PMID: 29598829
DOI: 10.1186/s13072-018-0182-4

[…] set out to completely characterise the methylation changes seen in the cell lines using the illumina infinium humanmethylation450 beadchip (450k) array platform [] and subsequent analysis using the rnbeads pipeline []. these approaches were chosen due to their high reproducibility and low inter-operator variability, ensuring the reliable and sensitive detection of alterations in methylation. […]

PMCID: 5820258
PMID: 29463802
DOI: 10.1038/s41467-018-03170-7

[…] quantified using the humanmethylationepic (epic) beadchip (illumina, ca, usa) according to the manufacturer’s instruction. raw idat files were processed in r (3.3.1) using the bioconductor package rnbeads 1.6.1. methylation β-values were normalized using the bmiq method in order to correct for potential bias in dna methylation measurements between type i and type ii probes. principle component […]

PMCID: 5802460
PMID: 29382824
DOI: 10.1038/s41398-017-0070-x

[…] non-cpg context, non-autosomal probes, probes with a snp mapping to the target cpg site or with three or more snps within the 50-mer probe (minor allele frequency (maf )> 0.01) (based on rnbeads package annotation), multi-mapping or polymorphic cpgs (maf > 0.01 in european population) reported in refs.,, and probes with missing rate ≥5% in final samples. prior to analysis, missing […]


To access a full list of publications, you will need to upgrade to our premium service.

RnBeads institution(s)
Max Planck Institute for Informatics, Saarbrücken, Germany; Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

RnBeads reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review RnBeads