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methylumi:Handle Illumina methylation data
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Maintained by Sean Davis. Last updated 5 months ago.
dnamethylationtwochannelpreprocessingqualitycontrolcpgisland
9 stars 9.90 score 89 scripts 9 dependentsbioc
lumi:BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Maintained by Lei Huang. Last updated 5 months ago.
microarrayonechannelpreprocessingdnamethylationqualitycontroltwochannel
6.26 score 294 scripts 5 dependents