missMethyl protocols

View missMethyl computational protocol

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missMethyl specifications

Information


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
Requirements
BiocStyle, edgeR, rmarkdown, knitr, R(>=2.3.0), tweeDEseqCountData, minfiData
Maintained Yes

Subtools


  • DiffVar
  • SWAN

Versioning


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Documentation


Maintainer


  • person_outline Belinda Phipson <>

Publications for missMethyl

missMethyl in pipelines

 (3)
2018
PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] 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 […]

2018
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] and detecting dmps or dmrs. when analyzing small dataset, minfi and methylumi are optimal choice to import data and sqn, bmiq and rcp may be proper to correcting the infinium i/ii bias. r package missmethyl is suitable for go term enrichment analysis and biological interpretation. in our view, minfi is a proper r package to import data, eliminate background and enmix package can be used […]

2017
PMCID: 5756244
PMID: 29058119
DOI: 10.1007/s00401-017-1773-z

[…] r package. logr ratio thresholds of ± 0.15 were used as a cutoff to determine gains and losses., gene set enrichment analysis of methylation data was carried out using the gsameth function in the missmethyl r package. differentially methylated positions (dmps) between group 1 and group 2 tumours were identified using the dmpfinder function in minfi. this list of dmps was then assayed […]


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missMethyl in publications

 (24)
PMCID: 5925605
PMID: 29740534
DOI: 10.3389/fonc.2018.00100

[…] tumors from normal samples., 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 […]

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

[…] minfi and methylumi are optimal choice when analyzing small dataset. bmiq and rcp are proper to correcting type bias and the normalized result of them can be used to discover dmps. r package missmethyl is suitable for go term enrichment analysis and biological interpretation., dna methylation is an important epigenetic modification which has shown numerous associations with biological […]

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

[…] 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 […]

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

[…] runs, an active proximity filter and a bonferroni correction for 169 factors were used as eforge parameters., 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., dna was extracted from 94 microdissected […]

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

[…] 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 […]


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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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