RnaSeqTutorial01

Introduction to Data Science tutorial based on learnr

Installation

In R do the following to install the dependencies

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

Then install the package using e.g. pak

if(!require("pak")){BiocManager::install("pak")}
pak::pkg_install("UPSCb/Tutorial_01_data_science_intro")

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_01_data_science_intro")

Getting started

This is the first 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("01_data_science_intro", package = "RnaSeqTutorial01")

Accessing the code

Tutorials

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

dir(system.file(package="RnaSeqTutorial01","tutorials"))

list.files(path=system.file(package="RnaSeqTutorial01","tutorials"),
           pattern="*.Rmd",
           recursive=TRUE)

Scripts

There is a script available in the script directory:

list.files(path=system.file(package="RnaSeqTutorial01","scripts"),
           pattern="*.R",
           recursive=TRUE)