Reference

Data and data metrics example inputs These are publicly available RNA-seq datasets in data and data metrics object formats. Half of them are data subsets (‘sub’). These were subsetted by selecting one out of ten genes from the full datasets. They can be used to quickly test the package functions and are shown in the example vignettes to reduce space.
soybean_cn	Normalized soybean cotyledon data
soybean_cn_metrics	Normalized soybean cotyledon metrics
soybean_ir	Raw soybean leaves iron-metabolism data
soybean_ir_metrics	Raw soybean leaves iron-metabolism metrics
soybean_cn_sub	Normalized and subsetted soybean cotyledon data
soybean_cn_sub_metrics	Normalized and subsetted soybean cotyledon metrics
soybean_ir_sub	Raw and subsetted soybean leaves iron-metabolism data
soybean_ir_sub_metrics	Raw and subsetted soybean leaves iron-metabolism metrics
SummarizedExperiment example inputs These are subsetted publicly available RNA-seq datasets in SummarizedExperiment object format.
se_soybean_cn_sub	Normalized and subsetted soybean cotyledon SummarizedExperiment
se_soybean_ir_sub	Raw and subsetted soybean leaves iron-metabolism SummarizedExperiment
SummarizedExperiment data formatting tools These functions manipulate SummarizedExperiment data format by reducing number of treatment pairs and number of genes.
convertSEPair()	Convert SummarizedExperiment to contain defined treatment pair
convertSESubsetGenes()	Convert SummarizedExperiment to only contain defined genes
Static plotting tools These functions plot RNA-seq data and optionally overlay differentially expressed genes (DEGs).
plotClusters()	Plot static parallel coordinate clusters
plotLitre()	Plot static litre plots
plotPCP()	Plot static parallel coordinate plots
plotSM()	Plot static scatterplot matrices
plotVolcano()	Plot static volcano plot
Interactive plotting tools These applications plot RNA-seq data and optionally overlay differentially expressed genes (DEGs).
plotLitreApp()	Plot interactive litre plots
plotPCPApp()	Plot interactive parallel coordinate plots
plotSMApp()	Plot interactive scatterplot matrices
plotVolcanoApp()	Plot interactive volcano plots