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Parent category Analysis
Description Fold change, differential expression
Component Version Inputs Outputs Description
CreateSQLiteIDs 0.1 geneList wIDs For a subset of genes, create a file with additional reference IDs.
DEan 0.4 expr, treatment array, diffExpr Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test.
DEGReport 1.1.1 deg, geneAnnotation, expr summary, genelist Creates a LaTeX report on differentially expressed genes (DEGs).
ExpressionExtremes 1.3 in out Selects differentially expressed genes using expression values as criterion.
ExprMixtureModel 1.4 expr, annot, groups stats, report, samplesets Provides a mixture model fit of two normal distributions for the given genes.
FoldChange 1.1 in out Selects differentially expressed genes using fold change as criterion.
SampleExpression 1.1 expr, groups indicator, logratio, deviation Creates a -1/0/1 matrix that indicates whether a given gene/probe is differentially expressed in individual samples.

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