templates-rmd-de

Differential expression analysis template

Quick start

Run with rmdCore

If you want only to get a copy of a template run:

rmdCore::run_template("pilm-bioiformatics/templates-rmd-de", ".")

Example run with all paramters:

install.packages("devtools")
devtools::install_github("pilm-bioinformatics/rmdCore")
library(rmdCore)
download.file("https://github.com/pilm-bioinformatics/templates-rmd-de/raw/master/data/se.rds", "se.rds")
run_template("pilm-bioinformatics/templates-rmd-de", 
             "working_dir",
             options = list(se_file = "se.rds",
                            output_dir = "test",
                            contrast = "condition.treated_vs_untreated, type.paired-end_vs_single-read",
                            metadata = c("condition", "type")
                            ),
              output_file = "test/de.html")

Run example data:

rmdCore::run_template("pilm-bioiformatics/templates-rmd-de", ".")
setwd("templates-rmd-de")
rmdCore::run_template(".", NULL, output_file = "docs/de.html")

Run with manually

Download the repository and get inside:

cd pilm-bioiformatics/templates-rmd-de

Run insde R:

rmarkdown::render("main.Rmd",
  params = list(se_file = "data/se.rds",
                output_dir = "test",
                contrast = "condition.treated_vs_untreated, type.paired-end_vs_single-read",
  output_file = "test/de.html")

Modify parameters to match your data.

Run with docker

docker run --rm -v `pwd`:/mnt/analysis --user bioc \
    -w /mnt/analysis \
    lpantano/templates-rmd-de Rscript -e  \
    'rmdCore::run_template(".", NULL, output_file = "docs/de.html")'

And use any of the previous commands.