single cell technologies

Welcome!

My field of study is in the development of single cell technologies and their applications to cancer early detection and neurodevelopment. A summary of the motivation and state of single cell methods for various regulatory features can be found here:

Background

• Corticogenesis
• Single cell HiC
• Single cell WGS
• Single cell ATAC
• Why single-cell analysis?
• Single cell MET

My full code for processing of various projects while working towards my graduate thesis in the O’Roak and Adey labs is available below. Some of the basic processing (bcl2fastq to generation of a counts matrix) was performed in our bash environment or with the Adey lab developed scitools helper functions. The rest was performed in either R or python environments.

sciATAC

• Organoids

s3 Assays

• s3 Pre-processing
• s3ATAC Analysis
• s3GCC Analysis
• s3WGS Analysis

Alternative Assays

• txci-ATAC

I joined CEDAR, at OHSU for roughly one year to begin my transistion into a cancer researcher. My actively developed code for projects there are available as well.

CEDAR Projects

• 10X Multiome Cell Lines
• 10X Multiome Tumor Phase 1
• 10X Multiome Tumor All Together
• 10X Multiome Tumor Preliminary
• NMTseq Annotations
• Cell Line NMTseq Analysis
• MOFA2 on NMTseq
• Breast Cancer NMTseq Analysis

More recently, I joined up with Nick Navin at MD Anderson to explore the effect of copy number variation on the epigenome.

MD Anderson Projects

• Environment Setup
• gccACT-seq Initial Test
• gccACT ONT Analysis
• gccACT-seq Wafergen Test
• metACT-seq Ligation Benchmarking
• WGD Analysis

Finally, I include some side projects from hobbies including 3D printing and rendering.

Side Projects

• 3D Topography of Oregon Mountains
• 3D Scatter Plots
• Auto-ideogram project
• DNA Builder
• Molecular renders

Have a look around!