BBS-230B (2024)
May 6, 2024 ยท View on GitHub
Bulk RNA-seq, May 6th, 2024
Learning objectives
- Explain common considerations when designing a bulk RNA-seq experiment
- List the steps involved in the analysis of a bulk RNA-seq dataset
- Discuss common challenges and how to overcome them
Lessons
- Experimental design (20 min)
- Raw data to counts workflow (25 min)
- Differential gene expression analysis (25 min)
- Functional analysis (20 min)
- Visualization of DE results (time permitting)
Single cell RNA-seq, May 8th, 2024
Learning objectives
- Explain common considerations when designing a single-cell RNA-seq experiment
- List the steps involved in the analysis of a single cell dataset
- List the key statistical concepts utilized for the analysis
Lessons
- Single cell RNA-seq (50 mins)
Resources (bulk RNA-seq)
- bulk RNA-seq "Part I" (FASTQ to count matrix) workshop
- Differential Gene Expression analysis workshop
- Planning a successfull bulk RNA-seq experiment
- DESeq2 vignette
- Functional analysis visualization
- Ggplot2 for functional analysis
Resources (Single cell RNA-seq)
- Single-cell RNA-seq workshop
- "How many cells are needed per sample for my single-cell experiment?"
- http://bioconductor.org/books/release/OSCA/
- https://liulab-dfci.github.io/bioinfo-combio/
- https://hemberg-lab.github.io/scRNA.seq.course/
- https://github.com/SingleCellTranscriptomics
- Seurat vignettes