Open the R Shiny interface
In R (or R Studio), open the R Shiny interface by running:
# Set up to your working directory
setwd("~path")
# Open the interface
library(sCCIgen)
run_interactive_sCCIgen()It will show you three tasks to choose from:
Task 1: I want to download a pre-simulated SRT dataset.
sCCIgen provides three pre-simulated datasets. You can
quickly check the data format and explore your analyses before spending
efforts on learning the package and simulating data. These datasets are
simulated based on normal breast snRNAseq, mouse brain SeqFISH+, and
human ovarian cancer MERFISH.
Here, select one example data and it will be downloaded to your working directory.
Task 2: I want to create a parameter file.
If you select Task 2, sCCIgen will first walk you
through (1) the selection of reference dataset, and (2) the additional
parameter determination questions to help you generate a parameter
file.
Playing with the decoy data may help get familiar with the simulator, while spending little time waiting for the simulation results. For simulation based on real datasets, users can also use our built-in real data by selection (5-7) or upload input data by selecting “user input”.