Single-cell RNA-seq data analysis workshop

Audience Computational skills required Duration
Biologists Introduction to R 2-day workshop (~10 hours of trainer-led time)

Description

This repository has teaching materials for a hands-on Introduction to single-cell RNA-seq analysis workshop. This workshop will instruct participants on how to design a single-cell RNA-seq experiment, and how to efficiently manage and analyze the data starting from count matrices. This will be a hands-on workshop in which we will focus on using the Seurat package using R/RStudio. Working knowledge of R is required or completion of the Introduction to R workshop.

Learning Objectives

These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.

Lessons

Click here for links to lessons and the proposed schedule

Installation Requirements

Applications

Download the most recent versions of R and RStudio for your laptop:

Packages for R

Note 1: Install the packages in the order listed below.

Note 2:  All the package names listed below are case sensitive!

Note 3: At any point (especially if you’ve used R/Bioconductor in the past), in the console R may ask you if you want to update any old packages by asking Update all/some/none? [a/s/n]:. If you see this, type “a” at the prompt and hit Enter to update any old packages. Updating packages can sometimes take quite a bit of time to run, so please account for that before you start with these installations.

Note 4: If you see a message in your console along the lines of “binary version available but the source version is later”, followed by a question, “Do you want to install from sources the package which needs compilation? y/n”, type n for no, and hit enter.

(1) Install the 7 packages listed below from CRAN using the install.packages() function.

  1. tidyverse
  2. Matrix
  3. RCurl
  4. scales
  5. cowplot
  6. BiocManager
  7. Seurat**

Please install them one-by-one as follows:

install.packages("tidyverse")
install.packages("Matrix")
install.packages("RCurl")
& so on ...

** If you have trouble installing Seurat, please install multtest using the following lines of code, then try installing Seurat again:

install.packages("BiocManager")

BiocManager::install("multtest")

(2) Install the 3 packages listed below from Bioconductor using the the BiocManager::install() function.

  1. SingleCellExperiment
  2. AnnotationHub
  3. ensembldb

Please install them one-by-one as follows:

BiocManager::install("SingleCellExperiment")
BiocManager::install("AnnotationHub")
& so on ...

(3) Finally, please check that all the packages were installed successfully by loading them one at a time using the library() function.

library(Seurat)
library(tidyverse)
library(Matrix)
library(RCurl)
library(scales)
library(cowplot)
library(SingleCellExperiment)
library(AnnotationHub)
library(ensembldb)

(4) Once all packages have been loaded, run sessionInfo().

sessionInfo()

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.