Package index
-
ExpressionResultSet-class - An S4 class to store differential expression results
-
consensusList() - consensusList: make a list of genes considered DE by at least 'threshold' tools
-
createExpressionResultSet() - Constructor for ExpressionResultSet
-
createNameFileOutput() - Build a file output name
-
expressionDefinition() - Identify DE genes by method-specific thresholds
-
frameAllGenes() - frameAllGenes
-
gse95077 - NCBI GEO access GSE95077 dataset
-
listDeByTool() - listDeByTool: creates a data.frame with genes (rows) and DE tools (columns). Each tool that identifies a gene as DE is marked with 1.
-
readCountFile() - Read table count File and creates a matrix from the given content file.
-
runDeseq2() - Execute DESeq2 DGE default analysis is configured to read only kallisto files, and count data
-
runEbseq() - Execute EBSeq gene Expression analysis
-
runEdger() - Execute edgeR expression Analisys
-
runExpression() - Make expression analysis of 7 tools, and return a list of results by each tool.
-
runKnowSeq() - Execute knowSeq differential Expression analyse
-
runLimma() - Execute edgeR expression Analisys
-
runNoiSeq() - Execute NOISeq gene Expression analysis
-
runSamSeq() - Execute SAMSeq gene Expression analysis to count data
-
show(<ExpressionResultSet>) - Show method for ExpressionResultSet
-
summary(<ExpressionResultSet>) - Summary method for ExpressionResultSet
-
upSetPlotTools() - UpSet Plot shows intersections by DE indications
-
writeResults() - Write a table or data.frame in defined output file