-
Notifications
You must be signed in to change notification settings - Fork 34
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)
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
. Note that the code in this 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.