run_dseqr | R Documentation |
Run dseqr application to explore single-cell and bulk RNA-seq datasets.
run_dseqr(
app_name,
data_dir,
tabs = c("Single Cell", "Bulk Data", "Drugs"),
pert_query_dir = file.path(data_dir, ".pert_query_dir"),
pert_signature_dir = file.path(data_dir, ".pert_signature_dir"),
gs_dir = file.path(data_dir, ".gs_dir"),
indices_dir = file.path(data_dir, ".indices_dir"),
tx2gene_dir = file.path(data_dir, ".tx2gene_dir"),
app_dir = system.file("app", package = "dseqr", mustWork = TRUE),
host = "0.0.0.0",
port = 3838,
logout_url = NULL,
is_local = is.null(logout_url),
test = FALSE,
is_example = FALSE
)
app_name |
Name of user folder in |
data_dir |
Directory containing app folders. By default also will contain folders
|
tabs |
Character vector of tabs to include in order desired. Must be subset of 'Single Cell', 'Bulk Data', and 'Drugs'. |
pert_query_dir |
Path to directory where pert query results (using CMAP02/L1000 as query signature) will be downloaded as requested. |
pert_signature_dir |
Path to directory where pert signatures for CMAP02/L1000 will be downloaded as requested. |
gs_dir |
Path to directory where gene to Gene Ontology maps produced by get_genego are saved. |
indices_dir |
Path to directory containing |
tx2gene_dir |
Path to directory containing transcript to gene maps produced by load_tx2gene. |
app_dir |
Directory containing shiny app files. Default is to use 'app' directory of installed dseqr package. Can be 'inst/app' if working from source code. |
host |
The IPv4 address that the application should listen on. Defaults
to the |
port |
The TCP port that the application should listen on. If the
|
logout_url |
URL used to log users out. Default is |
is_local |
Is dseqr running locally? If |
test |
Create a test with shinytest2? Default is |
is_example |
Is the app for demonstration purposes? If |
Runs dseqr app
if (interactive()) {
data_dir <- tempdir()
app_name <- 'example'
run_dseqr(app_name, data_dir)
}
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