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DESeq2.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with DESeq2 |
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DESeq2.length.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with DESeq2 with custom model matrix |
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DSS.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with DSS |
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EBSeq.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with EBSeq |
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NBPSeq.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with NBPSeq |
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NOISeq.prenorm.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with NOISeq |
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TCC.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with TCC |
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checkDataObject()
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Check a list or a compData object for compatibility with the differential expression functions interfaced by compcodeR |
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checkTableConsistency()
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Check consistency of input table to runComparison |
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check_compData()
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Check the validity of a compData object |
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check_compData_results()
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Check the validity of a compData result object |
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check_phyloCompData()
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Check the validity of a phyloCompData object |
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compData-class
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Class compData |
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compData()
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Create a compData object |
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compcodeR-package compcodeR
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RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods |
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convertListTocompData()
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Convert a list with data and results to a compData object |
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convertListTophyloCompData()
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Convert a list with data and results to a phyloCompData object |
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convertcompDataToList()
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Convert a compData object to a list |
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convertphyloCompDataToList()
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Convert a phyloCompData object to a list |
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edgeR.GLM.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with the edgeR GLM approach |
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edgeR.exact.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with the edgeR exact test |
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generateCodeHTMLs()
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Generate HTML file(s) containing code used to run differential expression analysis. |
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generateSyntheticData()
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Generate synthetic count data sets |
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lengthNorm.limma.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with length normalized counts + limma |
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lengthNorm.sva.limma.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with length normalized counts + SVA + limma |
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listcreateRmd()
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List available *.createRmd functions |
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logcpm.limma.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with limma after log-transforming the counts per million (cpm) |
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phyloCompData-class
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Class phyloCompData |
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phyloCompData()
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Create a phyloCompData object |
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phylolm.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with phylolm. |
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runComparison()
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Run the performance comparison between differential expression methods. |
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runComparisonGUI()
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A GUI to the main function for running the performance comparison between differential expression methods. |
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runComparisonShiny()
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A shiny-based GUI to the main function for running the performance comparison between differential expression methods. |
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runDiffExp()
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The main function to run differential expression analysis |
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show(<compData>)
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Show method for compData object |
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show(<phyloCompData>)
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Show method for phyloCompData object |
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sqrtcpm.limma.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with limma after square root-transforming the counts per million (cpm) |
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summarizeSyntheticDataSet()
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Summarize a synthetic data set by some diagnostic plots |
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ttest.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with a t-test |
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voom.limma.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with voom+limma |
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voom.ttest.createRmd()
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Generate a .Rmd file containing code to perform differential expression analysis with voom+t-test |