T2T chrY
GitHub: https://github.com/arangrhie/T2T-HG002Y
This GitHub repo contains all the code from Rhie, 2023.
I contributed to this work through the analysis of a variety of epigenetics datasets including CpG 5-methylcytosine measured with whole genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), PacBio, and ONT, as well as nanoNOMe GpC 5-methylcytosine data. Documentation for the analysis of this data can be found within the main GitHub repo here.
T2T epigenetics
GitHub: https://github.com/timplab/T2T-Epigenetics
This GitHub repo contains all the code from Gershman, 2022.
I contributed to this work through the generation of HG002 ultra-long nanoNOMe GpC data and the comparison of CHM13 methylation state to reduced representation bisulfite sequencing (RRBS) data from human embryos. Documentation for the analysis of the RRBS data can be found within the main GitHub repo here.
Analysis of public mouse ATAC-seq data
GitHub: https://github.com/pwh124/open_chromatin
Data: 
This Github repo and Zenodo data repo are associated with Hook and McCallion, 2020
Single-cell RNA-seq of dopaminergic neurons
Github: https://github.com/pwh124/sc-da-parkinsons
This Gitub repo contains code for analyses and figures associated with Hook, et al., 2018
Website: https://pwh124.github.io/sc-da-parkinsons/
I created this website from the Github repo above using the workflowr package. I wanted to create this website so that my data would be more accessible and reproducible.
Single-cell gene expression R Shiny App
I got the bug to create a Shiny App in 2017 in an attempt to mirror some of the websites made for various other single-cell RNA-seq projects at the time. While I think I did a half-way decent job, any feedback would be very welcomed.