Fig. 1
From: pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Overview of the pcaExplorer workflow. A typical analysis with pcaExplorer starts by providing the matrix of raw counts for the sequenced samples, together with the corresponding experimental design information. Alternatively, a combination of a DESeqDataSet and a DESeqTransform objects can be given as input. Specifying a gene annotation can allow displaying of alternative IDs, mapped to the row names of the main expression matrix. Documentation is provided at multiple levels (tooltips and instructions in the app, on top of the package vignette). After launching the app, the interactive session allows detailed exploration capability, and the output can be exported (images, tables) also in form of a R Markdown/HTML report, which can be stored or shared. (Icons contained in this figure are contained in the collections released by Font Awesome under the CC BY 4.0 license)