DIY.transcriptomics

Welcome to DIY Transcriptomics

A hybrid course covering best practices for bulk and single cell RNA-seq data analysis, with a primary focus on empowering students to be independent in the use of lightweight and open-source software and the R/bioconductor environment. Online curriculum is paired with in-person labs offered as CAMB714 at the University of Pennsylvania's School of Veterinary Medicine. The course is focused on infectious diseases, but concepts are applicable to any transcriptomics study.

Course overview

precourse lectures

A brief (but important!) overview that describes how the course is structured and how you can get the most from the material on this website.

Intro to RNAseq technology and data

precourse lectures

Learn all about Illumina's 'Sequencing by Synthesis' technology, and the steps involved in planning for a transcriptomics experiment.

Setting up your software environment

Lecture 1 • watch by Jan 18, 2023

In the first half of this lecture we'll discuss the open-source, cross-platform R/bioconductor software that we will use throughout the course. Then each student will set-up their own laptop to be a powerful, stand-alone bioinformatics workstation.

Ultra-fast read mapping with Kallisto

Lecture 2 • watch by January 25, 2023

In this class we'll finally get down to the business of using Kallisto for memory-efficient mapping of your raw reads. You'll carry out this mapping in class, right on your laptop, while we discuss what's happening under the hood. During this process, we'll touch on a range of topics, from reference files, to command line basics, and using shell scripts for automation and reproducibility.

Understanding RNAseq count data

Lecture 3 • watch by February 1, 2023

Now that we've aligned our reads, it's time to discuss units for measuring gene expression. We'll discuss differences between RPKM and TPM, and how these units relate to basic properties of your reference file and data. We'll also discuss normalization within and between samples. To conclude this class, we'll fire up RStudio and take a look at our first script.

Starting your R workflow

Lecture 4 • watch by February 8, 2023

We'll begin this class by reviewing how to access R packages and help documentation, as well as understanding the basic structure of an R script and RStudio project. We'll then access annotation data before reading our Kallisto results into R.

Wrangling gene expression data

Lecture 5 • watch by February 15, 2023

We'll begin this class by filtering and normalizing our data, all while using the ggplot2 graphing package to visualize the impact these changes have our data. You'll also be introduced to Hadley Wickham's philosophy of 'tidy data' by using the dplyr package, expanding your understanding of tools within the Tidyverse.

Data exploration

Lecture 6 • watch by February 22, 2023

In this class you'll learn about a variety of approaches exploring your data. You'll use multivariate statistical approaches such as Principal Component Analysis (PCA) to understand sources of variance in our data, while continuing to build your plotting skills by using ggplot2 to graph the results of PCA analyses. You'll also learn how to use the dplyr package to take control over our gene expression dataframes, allowing us to change, sort, filter, arrange and summarize large data sets quickly and easily using simple commands in R. We’ll discuss common missteps and how to identify sources of bias in transcriptional data sets.

Accessing public data

Lecture 7 • watch by March 1, 2023

In this class we’ll discuss how you can use R/Bioconductor to tap into vast amounts of RNAseq data available through the Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO).

Differential gene expression

Lecture 8 • watch by March 8, 2023

The ultimate goal of most transcriptional profiling experiments is to identify differentially expressed genes or transcripts. In this class, we'll dig into differential expression using the popular and venerable Limma package in R, while continuing to explore options for producing compelling plots from your differential expression results. Finally, we'll discuss a workflow for going beyond DGE analysis to look at differentail transcript (isoform) usage (DTU).

Module identification

Lecture 9 • watch by March 15, 2023

Coordinately expressed genes, or modules, often contain a more coherent functional signature. We'll discuss strategies for clustering expression data to identify these modules, setting the stage for downstream function enrichment analysis to be covered in the next class.

Functional enrichment analysis

Lecture 10 • watch by March 22, 2023

Now that you've identified differentially expressed genes, what do they mean and how do you begin to elucidate the biological pathways governed by these genes? To address this question, in this class you'll learn how to carry out functional enichment analyses using Gene Ontology and Gene Set Enrichment methods. You'll also explore different options for how to present your functional enrichment results.

Documenting your analyses with Rmarkdown

Lecture 11 • watch by March 29, 2023

In order to make your analysis pipeline transparent, in this class you'll use Rmarkdown and Knitr to wrap up all your code and outputs together in a dynamic document that can be placed in your lab notebook or published as a supplementary file in your manuscript.

Making your analysis portable and reproducible

Lecture 12 • watch by April 5, 2023

Reproducing an analysis requires more than just code. You need the original raw data, access to the appropriate programming languages, and application specific packages (and often specific versions of these packages). This poses a major impediment to reproducibility, even for researchers with a background in bioinformatics. To address this challenge, you'll learn how to 'containerize' your data, scripts and software, making it easy to share and rerun an entire analysis with the push of a button.

Single cell RNA-seq – principles and processing

Lecture 13 • watch by April 19, 2023

Now that you're comfortable with bulk RNA-seq data analysis, we'll shift our focus to the rapidly developing landscape of single cell RNA-seq (scRNA-seq). In this lecture, you'll learn about the underlying technology and we'll demonstrate how to process raw single cell data directly on your laptop (!) for importing into R/bioconductor.

Analysis of scRNA-seq data using R

Lecture 14 • watch by April 26, 2023

In this final lecture of the course, you'll learn to use Seurat to analyze scRNA-seq data, including carrying out dimensional reduction and display using UMAP, identifying cell clusters and cluster-specific marker genes, and how to integrate data from multiple samples.