RnaSeqTutorialXX

Using this template

1. Edit this README, change the title
2. Edit the R/RnaSeqTutorials-package.R file, line 1, 21, 23, 26, 27, 30 and 34
3. Update the README installation info (dependencies, github directory), you can use the code in R/RnaSeqTutorials-package.R to build the dependencies list.
4. Replace all XXX and XX with the tutorial and package name, respectively
5. Edit the DESCRIPTION, change the XX and XXX and add the dependencies
6. Configure the project option to enable Roxygen to build the doc
7. Build the doc with Roxygen
8. Check the package
9. Push to GH
10. Try to install using the instructions
11. (Fix and retry)
12. Remove this first section :-)

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TITLE TO CHANGE

Installation

In R do the following to install the dependencies

if(!require("BiocManager")) {install.packages("BiocManager")}
BiocManager::install(c("here","learnr"))

Then install the package using e.g. pak

if(!require("pak")){BiocManager::install("pak")}
pak::pkg_install("UPSCb/Tutorial_XXX")

Troubleshooting

If you get an error message stating: could not find tools necessary to compile a package, then:

• on Windows, you will need to install Rtools, select the right version for you R installation.

• on Mac OS, make sure that xcode is installed. In the terminal, run xcode-select --install.

If the above do not resolve the installation issue, then run this instead:

if(!require("pak")){BiocManager::install("devtools")}
devtools::install_github("UPSCb/Tutorial_XXX")

Getting started

This is the XXX in a series of tutorials.

1. 01_data_science_intro: an introduction to data science using the palmerpenguins package
2. 02_exploratory_data_analysis: the exploratory data analysis of a public RNA-Seq dataset
3. 03_differential_gene_expression: the differential expression DE analysis of the same dataset
4. 04_gene_set_enrichment_analysis: gene set enrichment analysis (GSEA) on the DE gene sets
5. 05_ensemble_gene_set_enrichment_analysis: ensemble GSEA of the DE gene sets and comparison to GSEA
6. 06_differential_transcript_usage: the differential transcript usage analysis of the same dataset
7. 07_non_model_organism_exploratory_data_analysis: the exploratory data analysis of a Norway spruce RNA-Seq dataset
8. 08_non_model_organism_differential_gene_expression: the differential expression DE analysis of the Norway spruce RNA-Seq dataset

To start the tutorial run:

learnr::run_tutorial("XXX", package = "RnaSeqTutorialXX")

Accessing the code

Tutorials

The tutorial is available as .Rmd files in the tutorials directory:

dir(system.file(package="RnaSeqTutorialXX","tutorials"))

list.files(path=system.file(package="RnaSeqTutorialXX","tutorials"),
           pattern="*.Rmd",
           recursive=TRUE)

Scripts

There may be script(s) available in the scripts directory:

list.files(path=system.file(package="RnaSeqTutorialXX","scripts"),
           pattern="*.R",
           recursive=TRUE)