/single_cell_analysis

Materials for a single cell analysis workshop (2014)

Primary LanguageR

Introduction to Single-cell RNA-Seq Analysis

Summary: These are the materials for a single-cell RNA-Seq analysis workshop.

Included are:

  • cut_and_paste.txt - You can cut/copy and paste code from this document into your RStudio console to work through the presentation. (On a windows machine word pad or RStudio worked best for opening this document.)

  • install_notes.txt - How to install the libraries in this presentation.

  • reading.txt - Some publications to get you started, have fun these are great reads!

  • references_and_tutorials.txt - References for information used in the presentation and online tutorials for further reading.

  • single_cell_analysis.Rpres - The presentation in RStudio format (the environment I used to build the presentation).

  • data/scde_results.txt - If you are using a windows machine, you will not be able to run SCDE; no worries. These are the results from the run shown in the presentation.

  • url_presentation.txt - URL for on-line presentation

Others:

  • data - data read in during the presentation

  • images - images for presentation

  • single_cell_analysis.css - formats the presenation

  • single_cell_analysis.md - The markdown used to make the presentation.

  • src - some code to reduce the amount of R code during the workshop. You are welcome to use the code as you need.

  • src/heatmap.3b.R - convenience code to make it easy to make a heatmap during the workshop

  • src/Module.R - helper functions which may be used in the presentation to reduce code.