Belinda Phipson

Belinda Phipson

1 packages on CRAN

2 packages on Bioconductor

missMethyl

bioconductor
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Normalisation and testing for differential variability and differential methylation for data from Illumina's Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.

statmod

cran
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A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes a number of advanced generalized linear model functions including new Tweedie and Digamma glm families and a secure convergence algorithm.

limma

bioconductor
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Data analysis, linear models and differential expression for microarray data.