3D RNA-seq App enables RNA-seq data analysis to be done only within 3 Days.

aggPvalue | Aggregate multiple p-values to a single p-value |

boxplotNormalised | Boxplot of expression distribution in each sample. |

check.mean.variance | Compare expression mean-variance trends before and after low... |

condition2design | Convert conditions to design matrix for linear regression |

counts2CPM | Convert read counts to counts per million reads (CPM) |

CPM.filter | Filter low expression based on CPM (count per million reads) |

data.error | Calculate standard deviation or standard errors |

DEvsDAS | Compare DE and DAS results |

distinct.color | Generate distinct colours |

fa2mapping | Generate transcript-gene mapping from transcriptome fasta... |

generate.report | Generate html, pdf and word report from Rmd (RMardkown) file |

getExample | Download example data for 3D RNA-seq analysis |

gg.color.hue | Generate HCL colours, which are the same to 'ggplot' default... |

gtf2mapping | Generate transcript-gene mapping from transcriptome gtf file |

iso.switch | Isoform switch analysis for time-series data |

limma.pipeline | Dfferential expression (DE) and alternative splicing (DAS)... |

list2dataframe | Convert list to data frame |

low.expression.filter | Filter low expressed transcripts and genes |

plot.abundance | Plot gene and transcript expression profiles |

plotEulerDiagram | Plot Euler diagram |

plotFlowChart | Plot flow-chart graph of DE and DAS results |

plotGO | Bar plot of GO annotation |

plotMeanVariance | Plot the mean-variance trend |

plotPCAind | Make principal component analysis (PCA) plot of individual... |

plotPWISnumber | Barplot of switch numbers in contrast groups |

plotTSIS | Plot time-series switches of a pair of isoforms |

plotTSISnumber | Barplot of switch numbers across time-points |

plotUpdown | Bar plot of up- and down-regulation |

plotVolcano | Volcano plot |

remove.batch | Estimate batch effects between biological replicates |

reorderClusters | Reorder the clusters according to their average exprssion |

rowmean | Calculate column mean of a matrix or data frame based on a... |

rowratio | Calculate column raito of a matrix or data frame based on a... |

run3DApp | Run 3D RNA-seq App |

score.filter | Filtering the scores for isoform switch |

set2 | Generate all possible logical relations between set x and y. |

sumarrays | Sum Over Replicate Arrays |

summaryDAStarget | Summary DAS genes and DTU transcripts |

summaryDEtarget | Summary DE genes and transcripts |

summaryStat | Merge two testing statistics |

switch.density | Density plot |

TPM.filter | Filter low expression based on TPM (transcript per million... |

transAbundance2PS | Calculate transcript PS (percent spliced) and DeltaPS from... |

trend.mean.variance | Estimate mean-variance trend of expression |

TSgroup2contrast | Generate contrast groups of time-series trend test |

ts.intersection | Searching for intersection points of two time-series |

ts.spline | Fit a time-series with spline curve |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.