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missMethyl specifications


Unique identifier OMICS_06802
Name missMethyl
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
BiocStyle, edgeR, rmarkdown, knitr, R(>=2.3.0), tweeDEseqCountData, minfiData
Maintained Yes


  • DiffVar
  • SWAN


No version available



  • person_outline Belinda Phipson

Publications for missMethyl

missMethyl citations


Genomic DNA Methylation Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues

PMCID: 5925605
PMID: 29740534
DOI: 10.3389/fonc.2018.00100

[…] To identify the gene ontology (GO) terms overrepresented in the genes harboring differentially methylated probes, a gene-set enrichment analysis was performed using the missMethyl package (), taking into account the number of CpG sites per gene. GO terms with a Bonferroni corrected p-value <0.01 were considered significant. Only the biological processes were reported […]


A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

BMC Bioinformatics
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] t there are differences among results of different methods, which maybe caused by the models they applying to normalization. Then the GO term enrichment analysis were analyzed with gometh function in missMethyl package. The GO terms of FDR ≤0.05 of five methods were got (see Table ) and the Venn diagram of GO terms obtained after normalization is shown in Fig. . RCP got the highest rate of common […]


Epigenome wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation

Clin Epigenetics
PMCID: 5824607
PMID: 29484035
DOI: 10.1186/s13148-018-0457-4

[…] he log2 ratio of the intensities of the methylated signal versus the unmethylated signal. Differential methylation analysis was performed using remove unwanted variation (RUVm) [], implemented in the missMethyl R package [] taking into account the twin relationships. RUVm is a data-driven method of controlling for unwanted technical and biological variation in regression analyses using an empirica […]


Hypomethylation of CYP2E1 and DUSP22 Promoters Associated With Disease Activity and Erosive Disease Among Rheumatoid Arthritis Patients

PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] , specifically the RefSeq gene track, CpG island track, and chromatin state segmentation by hidden Markov model tracks for 2 blood tissues (GM12878 and K562) .Pathway analysis was performed using the missMethyl R package in order to determine whether certain biologic pathways are associated with RA clinical outcomes . Enrichment for Gene Ontology (GO) terms was performed using genes that contained […]


Epigenome wide association studies identify DNA methylation associated with kidney function

Nat Commun
PMCID: 5668367
PMID: 29097680
DOI: 10.1038/s41467-017-01297-7

[…] Enrichment of GO terms and KEGG pathways was performed in R version 3.3.0 with the missMethyl package taking into account the number of CpG sites per gene and correcting for multiple testing using the methods of Benjamini and Hochberg. […]


Cross tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder

Nat Commun
PMCID: 5654961
PMID: 29066808
DOI: 10.1038/s41467-017-00868-y

[…] hat these CpG sites may strongly influence functional-type enrichment analysis of CpG sites, and these CpG sites were not examined in the fetal brain meQTL lists. We used the gometh() function in the MissMethyl R package, which maps 450k DNAm sites to their nearest gene, and corrects for bias due to non-uniform coverage of genes on the 450k. We further ran nominally significant (hypergeometric tes […]

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missMethyl institution(s)
Bioinformatics Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
missMethyl funding source(s)
This work was funded through Victorian State Government Operational Infrastructure Support and NHMRC grants APP1051481, APP1051402.

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