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      Fall single cell RNA sequencing workshop @ UCSF

Home
Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics Perspective?
Experimental Design and Cost Estimation
Introduction to Command-Line and the Cluster
Logging in and Transferring Files
Intro to Command-Line
Advanced Command-Line (extra)
Running jobs on the Cluster and using modules
Intro to R and Rstudio
Getting Started
Intro to R
Prepare Data in R (extra)
Data in R (extra)
Data Reduction
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Guest lecture by Dr. Gerald Quon
Prepare Single Cell Alignment
Single Cell Alignment (scAlign)
Support
Cheat Sheets
Software and Links
Scripts
ETC
Closing thoughts
Workshop Photos
Github
Biocore website

Create a new RStudio project

Open RStudio and create a new project, for more info see https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects

Learn more about packrat see https://rstudio.github.io/packrat/

Set some options and make sure the packages Seurat, sva, ggplot2, dplyr, limma, topGO, WGCNA are installed (if not install it), and then load them and verify they all loaded correctly.

In the R console run the following commands


if (!any(rownames(installed.packages()) == "Seurat")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("Seurat")
}
library(Seurat)

if (!any(rownames(installed.packages()) == "sva")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("sva")
}
library(sva)

if (!any(rownames(installed.packages()) == "scran")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("scran")
}
library(scran)

if (!any(rownames(installed.packages()) == "ggplot2")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("ggplot2")
}
library(ggplot2)

if (!any(rownames(installed.packages()) == "dplyr")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("dplyr")
}
library(dplyr)

if (!any(rownames(installed.packages()) == "knitr")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("knitr")
}
library(knitr)

if (!any(rownames(installed.packages()) == "kableExtra")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("kableExtra")
}
library(kableExtra)

if (!any(rownames(installed.packages()) == "limma")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("limma")
}
library(limma)

if (!any(rownames(installed.packages()) == "biomaRt")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("biomaRt")
}
library(biomaRt)

if (!any(rownames(installed.packages()) == "topGO")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("topGO")
}
library(topGO)

if (!any(rownames(installed.packages()) == "org.Mm.eg.db")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("org.Mm.eg.db")
}
library(org.Mm.eg.db)

if (!any(rownames(installed.packages()) == "WGCNA")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("WGCNA")
}
library(WGCNA)

sessionInfo()

Download the template Markdown workshop document PART1 and open it.

In the R console run the following command

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019-Fall-single-cell-RNA-sequencing-Workshop-UCSF/master/scrnaseq_analysis/scRNA_Workshop-PART1.Rmd", "scRNA_Workshop-PART1.Rmd")

Download the data for the workshop, extract it.

In the R console run the following command.

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019-Fall-single-cell-RNA-sequencing-Workshop-UCSF/master/scrnaseq_analysis/expression_tables_cellrangerV3.zip", "expression_tables_cellrangerV3.zip")

Edit the file YAML portion

The top YAML (YAML ain’t markup language) portion of the doc tells RStudio how to parse the document.

---
title: "Single Cell RNAseq Part 1"
author: your_name
date: current_date
output:
    html_notebook: default
    html_document: default
---