Visualizing results with iSEE

The objects stored in the output file of the workflow (<output_directory>/outputR/shiny_sce.rds) can be directly used as input to the iSEE package in order to generate a shiny application where the results can be viewed. After installing iSEE, the following code will start a shiny application where you can browse the results:

library(iSEE)

sce <- readRDS("<output_directory>/outputR/shiny_sce.rds")

# sce on gene level
sce_g <- sce$sce_gene

# sce on transcript level
sce_t <- sce$sce_tx

# for example to see results on gene level
app <- iSEE(sce_g)
shiny::runApp(app)

Further customization

The iSEE package is highly customizable and full details are available from the package landing page: http://bioconductor.org/packages/iSEE.

An example panel customization with a set of standard RNA-seq visualizations is provided in the chiron_realdataworkflow branch in E-MTAB-7029/run_iSEE.R. If you want to become familiar with iSEE customization, you can download the precomputed shiny_sce.rds object and 6 bigwig files which has file names starting with Q10. These files corresponding to the E-MTAB-7029 data set. Before running the script, you have to specify the path to the downloaded shiny_sce.rds and 6 bigwig files on line 4 and 38 of run_iSEE.R.

Note that the code in the E-MTAB-7029/run_iSEE.R script is adapted to the E-MTAB-7029 data set (e.g., in terms of file paths, reference files, sample IDs and contrasts of interest), and thus should only be considered as an example.