Users can export/save their dataset after analyzing with SCTK, in three different formats:
To view detailed instructions on how to export data, please select ‘Interactive Analysis’ for exporting through the shiny application or ‘Console Analysis’ for exporting through the R console from the tabs below:
To export data through the user-interface, users should open up the “Export Single Cell Data” tab as shown above.
To save the analysis to RDS file, users need to:
The simplest steps to save the analysis to AnnData format is similar as how users save an RDS file. To save the analysis to RDS file, users need to:
For Python’s AnnData object, there are a few more specifications.
Similarly,
As mentioned at the beginning of the documentation, there will be several files for different information being saved. SCTK will create a directory under the path that users select at the first step, named by “File prefix,” all text files will be stored in this folder.
For additional specifications:
As how SCTK is designed, we assume users are attempting to save their data already in a SingleCellExperiment object:
Directly saving the object to RDS file
saveRDS(sce, "sce_exported.rds")
Exporting to AnnData (H5AD file)
exportSCEtoAnnData(sce)
Exporting to flat files
exportSCEtoFlatFile(sce)
Exporting as Seurat object
exportSCEToSeurat(sce)
For detailed specifications, please click on the function name and look at the reference page.