Man pages for vivekbhr/vivlib
An R package for useful bioinformatics wrappers
| annotate_DEoutput | annotate the output file from Differential Expression wrapper |
| Camera_plotbubble | Make a bubble plot for CAMERA output |
| clusterDEgenes | Cluster DE genes by fold change from multiple files |
| DESeq_wrapper | A Wrapper for DESeq2 over featurecounts output |
| EdgeR_wrapper | A Wrapper for EdgeR over featurecounts output |
| fcount_meantransform | Transform a featurecount output to a data frame of... |
| fetch_annotation | Fetch annotation from ENSEMBL ID to gene ID from Biomart |
| getIntrons_byGenes | Get introns by genes |
| makeVoomInput | Make Voom transformed input for BarCodePlot and ROAST test |
| plotBarCodes | Perform ROAST and make BarCodePlot using a voom transformed... |
| plotDEgeneOverlap | plot intersections of list of DE genes from multiple DESeq2... |
| plot_fCountSummary | Plot the output of featureCounts summary |
| plotHeatmap | Plot heatmap of raw counts for top DEgenes using edgeR/DESeq2... |
| plotPathway | Plot DE output on a selected KEGG pathway map |
| plotStackedBars | Plot Stacked barchart of DE genes using edgeR/DESeq2 output |
| plotVolcano | Make an informative volcano plot using edgeR/DESeq2 output |
| runCamera | A wrapper over CAMERA test. |
| spia_plotBubble | Make a bubblePlot for SPIA pathway output |
| spia_wrapper | A wrapper over SPIA pathway perturbation analysis for mouse... |
| splitBAM | Split a bam file by given criteria |
