Man pages for wyguo/ThreeDRNAseq
3D RNA-seq App enables RNA-seq data analysis to be done only within 3 Days.

aggPvalueAggregate multiple p-values to a single p-value
boxplotNormalisedBoxplot of expression distribution in each sample.
check.mean.varianceCompare expression mean-variance trends before and after low...
condition2designConvert conditions to design matrix for linear regression
counts2CPMConvert read counts to counts per million reads (CPM)
CPM.filterFilter low expression based on CPM (count per million reads)
data.errorCalculate standard deviation or standard errors
DEvsDASCompare DE and DAS results
distinct.colorGenerate distinct colours
fa2mappingGenerate transcript-gene mapping from transcriptome fasta...
generate.reportGenerate html, pdf and word report from Rmd (RMardkown) file
getExampleDownload example data for 3D RNA-seq analysis
gg.color.hueGenerate HCL colours, which are the same to 'ggplot' default...
gtf2mappingGenerate transcript-gene mapping from transcriptome gtf file
iso.switchIsoform switch analysis for time-series data
limma.pipelineDfferential expression (DE) and alternative splicing (DAS)...
list2dataframeConvert list to data frame
low.expression.filterFilter low expressed transcripts and genes
plot.abundancePlot gene and transcript expression profiles
plotEulerDiagramPlot Euler diagram
plotFlowChartPlot flow-chart graph of DE and DAS results
plotGOBar plot of GO annotation
plotMeanVariancePlot the mean-variance trend
plotPCAindMake principal component analysis (PCA) plot of individual...
plotPWISnumberBarplot of switch numbers in contrast groups
plotTSISPlot time-series switches of a pair of isoforms
plotTSISnumberBarplot of switch numbers across time-points
plotUpdownBar plot of up- and down-regulation
plotVolcanoVolcano plot
remove.batchEstimate batch effects between biological replicates
reorderClustersReorder the clusters according to their average exprssion
rowmeanCalculate column mean of a matrix or data frame based on a...
rowratioCalculate column raito of a matrix or data frame based on a...
run3DAppRun 3D RNA-seq App
score.filterFiltering the scores for isoform switch
set2Generate all possible logical relations between set x and y.
sumarraysSum Over Replicate Arrays
summaryDAStargetSummary DAS genes and DTU transcripts
summaryDEtargetSummary DE genes and transcripts
summaryStatMerge two testing statistics
switch.densityDensity plot
TPM.filterFilter low expression based on TPM (transcript per million...
transAbundance2PSCalculate transcript PS (percent spliced) and DeltaPS from...
trend.mean.varianceEstimate mean-variance trend of expression
TSgroup2contrastGenerate contrast groups of time-series trend test
ts.intersectionSearching for intersection points of two time-series
ts.splineFit a time-series with spline curve
wyguo/ThreeDRNAseq documentation built on July 11, 2019, 6:06 p.m.