Please, contribute with your improvements. I am sure you have something to add.
root = "https://github.com/hbc/hbcABC/tree/master/inst/rmarkdown/Rscripts/singlecell" # root = "../../inst/rmarkdown/Rscripts/singlecell" dir.create("reports")
simple_qc_single_cell
is a template to run a fast QC with ggplot code
to modify the plots as needed.
To create the template, use the Rstudio menu as for any other template or:
source = file.path(system.file("rmarkdown", package="hbcABC"), "templates", "sinple_qc_single_cell", "skeleton", "skeleton.rmd") file.copy(source, "reports/simple_qc_sc.rmd")
The next step is to run the normalization, scaling and clustering that are high demand in computation time and memory.
To run this analysis please read the documentation from our knowledgebase repo
If you get to have these two objects:
These objects will be used by seurat_clustering_single_cell
to perform
best practices as described by seurat tutorial.
source = file.path(system.file("rmarkdown", package="hbcABC"), "templates", "seurat_clustering_single_cell", "skeleton", "skeleton.rmd") file.copy(source, "reports/seurat_clustering.rmd")
system("rm -rf reports") system("rm -rf *.r")
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