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      Single Cell RNA-Seq Analysis

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Support
Slack
Zoom
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
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
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Create a new RStudio project

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

Learn more about (renv)[https://rstudio.github.io/renv/articles/renv.html]

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 (!requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
}

if (!any(rownames(installed.packages()) == "rmarkdown")){
  BiocManager::install("rmarkdown")
}

if (!any(rownames(installed.packages()) == "tinytex")){
  BiocManager::install("tinytex")
}

if (!any(rownames(installed.packages()) == "Seurat")){
  BiocManager::install("Seurat")
}

if (!any(rownames(installed.packages()) == "hdf5r")){
  BiocManager::install("hdf5r")
}

if (!any(rownames(installed.packages()) == "knitr")){
  BiocManager::install("knitr")
}

if (!any(rownames(installed.packages()) == "kableExtra")){
  BiocManager::install("kableExtra")
}

if (!any(rownames(installed.packages()) == "ggplot2")){
  BiocManager::install("ggplot2")
}

if (!any(rownames(installed.packages()) == "dplyr")){
  BiocManager::install("dplyr")
}

if (!any(rownames(installed.packages()) == "reshape2")){
  BiocManager::install("reshape2")
}

if (!any(rownames(installed.packages()) == "biomaRt")){
  BiocManager::install("biomaRt")
}

if (!any(rownames(installed.packages()) == "org.Hs.eg.db")){
  BiocManager::install("org.Hs.eg.db")
}

if (!any(rownames(installed.packages()) == "limma")){
  BiocManager::install("limma")
}

if (!any(rownames(installed.packages()) == "topGO")){
  BiocManager::install("topGO")
}

if (!any(rownames(installed.packages()) == "sva")){
  BiocManager::install("sva")
}

if (!any(rownames(installed.packages()) == "scran")){
  BiocManager::install("scran")
}

if (!any(rownames(installed.packages()) == "WGCNA")){
  BiocManager::install("WGCNA")
}

## All of thse should now load without error.

library(rmarkdown)
library(tinytex)
library(Seurat)
library(hdf5r)
library(knitr)
library(kableExtra)
library(ggplot2)
library(dplyr)
library(reshape2)
library(biomaRt)
library(limma)
library(topGO)
library(org.Hs.eg.db)
library(sva)
library(scran)
library(WGCNA)

sessionInfo()

Download the template Markdown workshop document PART1 and open it.

In the R console run the following command to download part 1 of data analysis

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-August-Single-Cell-RNA-Seq-Analysis/master/data_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 to download and extract the dataset (Little over 1Gb file.

options(timeout=1200)
download.file("https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/4vn7r610cf5d5dv/intro2singlecell_March2021.zip", "intro2singlecell_March2021.zip")
system("unzip intro2singlecell_March2021.zip") # works in Linux and Mac, not sure about Windows"

If you timed out on the download, increase 1200 to something higher. If the system command didn’t work to extract the zip file, navigate to the folder you downloaded the data in and manually unzip the archive file

The Dataset will only be available for download during this course

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

Your RStudio should look something like this

RStudio

Now spend a few minutes navigating through our data, how may samples are there? Find the hdf5 file and the matrix files. View the html files and lets discuss.