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-single-cell-RNA-sequencing-Workshop-UCD_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-single-cell-RNA-sequencing-Workshop-UCD_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
---