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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.

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missMethyl versioning

No versioning.

missMethyl classification

missMethyl specifications

Software type:
Suite
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
missMethyl version 1.2.0
Requirements:
R (>= 2.3.0)
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

Publications

  • (Phipson et al., 2015) missMethyl: an R package for analysing methylation data from Illumina's HumanMethylation450 platform. Bioinformatics.
    PMID: 26424855
  • (Phipson and Oshlack, 2014) DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging. Genome biology.
    PMID: 25245051
  • (Maksimovic et al., 2012) SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome biology.
    PMID: 22703947

missMethyl support

Maintainer

Credits

Institution(s)

Bioinformatics Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, 50 Flemington Road, Parkville, Victoria, 3052, Australia

Funding source(s)

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

Link to literature

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