Single-cell RNA-seq data analysis

This GitHub repository contains the files for the single-cell RNA-sequencing data analysis workshop from PSL winter school 2021 of monday afternoon.

Started on 2021-02-04.

The workshop website is available here: https://psl-winter-school-2021.github.io/01-monday-workshop-rna/introdution.html

Directory structure

• root
  • R Markdown analysis files (.Rmd files)
  • Configuration files (files starting by an underscore)
• docs
  • Rendered analysis reports (.html files)
  • Ouput images (.png files in docs/01-monday-workshop-rna_files/figure-html)
• data - Raw data used for the analysis

Data

Input data include the file GSM2494785_dge_mel_rep3.txt in the folder data/data_day1. This is a public single-cell RNA-seq count matrix extracted from the Karaiskos et al. paper.
You can download all the paper data from the GEO website with accession number GSE95025.

Modify notebook

If you want to modify the notebook, you need to:

1. Clone or download this repository (green button “code” on the top right of your screen).
2. Depends on which interface your use:
   • if you use RStudio open the 01-monday-workshop-rna.Rproj and then the 01-single_cell_intro.Rmd
   • if you use the terminal directly open 01-single_cell_intro.Rmd in your favorite text editor.

Build Notebook

To run the notebook and create the corresponding html files, you have two options:

• In RStudio, click the knit button
• In terminal, run the script build.sh with the command:

bash _build.sh

The output will be stored in the docs folder.