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consensusList()
- consensusList: make a list of genes was consider DE by threshold tools
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createNameFileOutput()
- Build a file output name
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expressionDefinition()
- Define who genes are deferentially expressed by method
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frameAllGenes()
- frameAllGenes
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gse95077
- NCBI GEO access GSE95077 dataset
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listDeByTool()
- listDeByTool: makes a data.frame with genes (lines) and all executed DE tool. Each tool that identify gene as DE, are marked by 1.
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readCountFile()
- Read table count File and creates a matrix from the given content file.
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runDeseq2()
- Execute DESeq2 DGE default analysis is configured to read only kallisto files, and count data
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runEbseq()
- Execute EBSeq gene Expression analysis
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runEdger()
- Execute edgeR expression Analisys
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runExpression()
- Make expression analysis of 7 tools, and return a list of results by each tool.
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runKnowSeq()
- Execute knowSeq differential Expression analyse
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runLimma()
- Execute edgeR expression Analisys
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runNoiSeq()
- Execute NOISeq gene Expression analysis
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runSamSeq()
- Execute SAMSeq gene Expression analysis to count data
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upSetPlotTools()
- UpSet Plot shows intersections by DE indications
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writeResults()
- Write a table or data.frame in defined output file