Chapter 1
Foundations
1: Getting Started with R & RStudio
Chapter 2
Data Structures
2: R Data Structures & Factors
Chapter 3
Logic & Functions
3: Control Flow & Custom Functions
Chapter 4
Data Wrangling
4: Tidyverse Biological Wrangling
Chapter 5
Genomic File I/O
5: Biological File I/O & Formats
Chapter 6
Visualization
6: Publication Figures with ggplot2
Chapter 7
Bioconductor Core
7: Bioconductor Core & GenomicRanges
Chapter 8
Biostatistics
8: Statistical Hypothesis Testing
Chapter 9
Transcriptomics
9: Bulk RNA-Seq with DESeq2
Chapter 10
Clustering & Heatmaps
10: Omics Heatmaps & Clustering
Chapter 11
Functional Genomics
11: Pathway & GO Enrichment
Chapter 12
Single-Cell Omics
12: Single-Cell RNA-Seq with Seurat
Chapter 13
Capstone & Reproducibility
13: Quarto & R Markdown Reports
Peer-Reviewed Foundations
Seminal peer-reviewed benchmarks and methodology literature
📚 Foundational Literature & Methodology Benchmarks
Bioconductor Architecture
- Huber W, Carey VJ, Gentleman R, et al. (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12(2):115–121. doi:10.1038/nmeth.3252
- Lawrence M, Huber W, Pagès H, et al. (2013). Software for computing and annotating genomic ranges (GenomicRanges). PLOS Comput Biol 9(8):e1003118. doi:10.1371/journal.pcbi.1003118
- Gentleman RC, Carey VJ, Bates DM, et al. (2004). Bioconductor: open software development for genomics and bioinformatics. Genome Biol 5(10):R80. doi:10.1186/gb-2004-5-10-r80
Differential Testing & Heatmaps
- Love MI, Huber W, Anders S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. doi:10.1186/s13059-014-0550-8
- Gu Z, Eils R, Schlesner M. (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32(18):2847–2849. doi:10.1093/bioinformatics/btw313
- Robinson MD, McCarthy DJ, Smyth GK. (2010). edgeR: a Bioconductor package for differential expression analysis. Bioinformatics 26(1):139–140. doi:10.1093/bioinformatics/btp616
Visualization & Single-Cell
- Wickham H. (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. doi:10.1007/978-3-319-24277-4
- Hao Y, Stuart T, Kowalski MH, et al. (2024). Dictionary learning for integrative, multimodal and scalable single-cell analysis (Seurat v5). Nat Biotechnol 42:293–304. doi:10.1038/s41587-023-01767-y
- Allaire J, Xie Y, Dervieux C, et al. (2022). Quarto: An open-source scientific and technical publishing system. Posit Software. doi:10.5281/zenodo.5960048