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missMethyl | Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips

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Performs normalisation, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450K array. The functions have been written to complement the limma package and are compatible with data objects from minfi, methylumi and edgeR. Detects differential variability for individual CpG sites in methylation data. DiffVar is available as a function in the missMethyl Bioconductor R package, and depends on the limma framework.

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missMethyl classification

missMethyl specifications

Unique identifier:
OMICS_06802
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.2.0
Maintained:
Yes

Subtools

  • DiffVar
  • SWAN

missMethyl distribution

versioning

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No versioning.

missMethyl support

Documentation

Maintainer

  • Belinda Phipson <>

Credits

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Publications

Institution(s)

Bioinformatics Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia

Funding source(s)

This work was funded through Victorian State Government Operational Infrastructure Support and NHMRC grants APP1051481, APP1051402.

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