MethylAid specifications

Information


Unique identifier OMICS_05457
Name MethylAid
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, stats, RColorBrewer, grid, graphics, BiocGenerics, Biobase, utils, grDevices, SummarizedExperiment, ggplot2, BiocParallel, gridBase, matrixStats, shiny, hexbin, R(>=3.4), minfi(>=1.22.0)
Maintained Yes

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Publication for MethylAid

MethylAid in publications

 (14)
PMCID: 5877863
PMID: 29601581
DOI: 10.1371/journal.pone.0194938

[…] the study was approved by the academic medical center research ethics board (ccmo: nl45496.018.13)., primary quality control (qc) on the raw 450k dataset was performed using the r shiny package methylaid (version 1.4.0)[]. methylaid is a user- friendly visual and interactive web application enabling detection of bad quality samples using sample-dependent and sample-independent control […]

PMCID: 5852574
PMID: 29419728
DOI: 10.3390/genes9020078

[…] system. twin pairs were analyzed on the same array. the three datasets were analyzed on different occasions., data preprocessing and quality control was performed in line with [] using the r-package methylaid. samples not meeting the quality requirements were excluded. probes with detection p-value >0.01, no signal, or bead count <3 were treated as missing. cpg sites with more than 5% […]

PMCID: 5792223
PMID: 29399631
DOI: 10.1126/sciadv.aao4364

[…] but were randomly assigned to either the left or right column of the 450k array. we assessed data quality using both sample-dependent and sample-independent quality metrics using the r package methylaid (). bisulfite conversion efficiency was assessed using the dedicated 450k probes and sequencing the igf2 dmr0 of a random set of samples. we remeasured a subset of the genotypes measured […]

PMCID: 5740718
PMID: 29299071
DOI: 10.1186/s13148-017-0427-2

[…] beadchips (illumina) array according to the manufacturer’s protocol. quality control for obtained dna methylation data was performed with two different pipelines, a combination of methylaid [] and minfi tools []. probes with low bead count (< 3 beads), high detection p value (> 0.01), and zero signal and missing in > 5% of samples were removed from further analysis. […]

PMCID: 5733014
PMID: 29311901
DOI: 10.3389/fnagi.2017.00413

[…] beadchips (illumina, san diego, ca, usa) array according to manufacturer's protocol. obtained dna methylation data was subjected to quality control with two different pipelines, combination of methylaid (van iterson et al., ) and minfi tools (aryee et al., ). probes with low bead count (<3 beads), high detection p-value (>0.01), zero signal, missing in >5% of samples […]


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MethylAid institution(s)
Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
MethylAid funding source(s)
This work was funded by the Biobank-based Integrative Omics Study (BIOS) Consortium funded by BBMRI-NL, a Research Infrastructure financed by the Netherlands Organization for Scientific Research (NWO 184.021.007) and partially supported by the European Union’s Seventh Framework Program (FP7/2007-2011) under grant agreement No. 259679 (IDEAL).

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