In hbc/hbcABC: Rmarkdown templates for bioinformatic analysis

Single cell templates

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")

QC

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.

Clustering with Seurat

To run this analysis please read the documentation from our knowledgebase repo

If you get to have these two objects:

• seurat_pre_regress.rds
• seurat_tsne.rds

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")

hbc/hbcABC documentation built on Sept. 5, 2019, 9:51 p.m.