Last data update: 2014.03.03
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SMO (statistical methods ontology)
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Images
classifyTests
(Package: limma ) :
Multiple Testing Genewise Across Contrasts
For each gene, classify a series of related t-statistics as up, down or not significant.
● Data Source:
BioConductor
● Keywords: htest
● Alias: FStat, classifyTestsF, classifyTestsP, classifyTestsT
●
0 images
contrastAsCoef
(Package: limma ) :
Reform a Design Matrix to that Contrasts Become Coefficients
Reform a design matrix so that one or more coefficients from the new matrix correspond to specified contrasts of coefficients from the old matrix.
● Data Source:
BioConductor
● Keywords: regression
● Alias: contrastAsCoef
●
0 images
contrasts.fit
(Package: limma ) :
Compute Contrasts from Linear Model Fit
Given a linear model fit to microarray data, compute estimated coefficients and standard errors for a given set of contrasts.
● Data Source:
BioConductor
● Keywords: htest
● Alias: contrasts.fit
●
0 images
controlStatus
(Package: limma ) :
Set Status of each Spot from List of Spot Types
Determine the type (or status) of each spot in the gene list.
● Data Source:
BioConductor
● Keywords: IO
● Alias: controlStatus
●
0 images
decideTests
(Package: limma ) :
Multiple Testing Across Genes and Contrasts
Classify a series of related t-statistics as up, down or not significant. A number of different multiple testing schemes are offered which adjust for multiple testing down the genes as well as across contrasts for each gene.
● Data Source:
BioConductor
● Keywords: htest
● Alias: decideTests
●
0 images
detectionPValues
(Package: limma ) :
Detection P-Values from Negative Controls
Compute the proportion of negative controls greater than each observed expression value. Particularly useful for Illumina BeadChips.
● Data Source:
BioConductor
● Keywords: background correction, illumina beadchips
● Alias: detectionPValues, detectionPValues.EListRaw, detectionPValues.default
●
0 images
diffSplice
(Package: limma ) :
Test for Differential Splicing
Given a linear model fit at the exon level, test for differences in exon retention between experimental conditions.
● Data Source:
BioConductor
● Keywords: rna-seq
● Alias: diffSplice
●
0 images
dim
(Package: limma ) :
Retrieve the Dimensions of an RGList, MAList or MArrayLM Object
Retrieve the number of rows (genes) and columns (arrays) for an RGList, MAList or MArrayLM object.
● Data Source:
BioConductor
● Keywords: array
● Alias: dim.EList, dim.EListRaw, dim.MAList, dim.MArrayLM, dim.RGList, length.EList, length.EListRaw, length.MAList, length.MArrayLM, length.RGList
●
0 images
dimnames
(Package: limma ) :
Retrieve the Dimension Names of an RGList, MAList, EList, EListRaw or MArrayLM Object
Retrieve the dimension names of a microarray data object.
● Data Source:
BioConductor
● Keywords: array
● Alias: dimnames.EList, dimnames.EListRaw, dimnames.MAList, dimnames.MArrayLM, dimnames.RGList, dimnames<-.EList, dimnames<-.EListRaw, dimnames<-.MAList, dimnames<-.RGList
●
0 images
dupcor
(Package: limma ) :
Correlation Between Duplicates
Estimate the correlation between duplicate spots (regularly spaced replicate spots on the same array) or between technical replicates from a series of arrays.
● Data Source:
BioConductor
● Keywords: multivariate
● Alias: duplicateCorrelation
●
0 images