My thesis

• My thesis: Bioinformatic analysis of complex, high-throughput genomic and epigenomic data in the context of CD4⁺ T-cell differentiation and diagnosis and treatment of transplant rejection
• Slides for my defense talk: The slides for my dissertation defense, mainly covering Chapter 2 of my thesis

Interesting sub-folders

Each folder showcases a different project or aspect of my work in the Salomon lab.

• Teaching: Teaching materials for my lecture and lab on introductory RNA-seq analysis
• CD4: Examples relating to my CD4 memory RNA-seq & ChIP-seq project
• 450k: Examples relating to analysis of Illumina 450k DNA methylation arrays
• Pathways: Examples of gene set and pathway analysis for RNA-seq data
• globin: Examples of my work in demonstrating the performance of a new globin blocking protocol for RNA-seq of blood tissues
• fRMA: Examples and code from my work creating a custom frozen RMA reference to provide a stable normalization for machine learning applications

Presentations

• DGE Presentation.pdf: comparing edgeR, DESeq, and limma on both a conceptual and practical level
• Advanced RNA-seq Analysis.pdf: On the advanced features provided by limma for RNA-seq analysis
• Reproducible Workflow Presentation.pdf: Showcases the use of Snakemake for building a reproducible analysis

Other files

• Classifier Math Write-up.pdf: A short write-up to explain the mathematical principles behind the classifier method used in a machine learning project
• blockbuster-pipeline.R.html: R code for clustering small RNA reads into clusters using Blockbuster
• mdsplots-multidim.pdf: A PCA plot of RNA-seq data for C. elegans samples with and without a drug that retards the aging process, demonstrating smaller age-related changes with the drug (for this paper)