Ethan Holleman's repositories
ethanholleman.github.io
Source code for Ethan Holleman's personal website.
ADARColab
Repo for in vitro ADAR deamination of R-loops project related files
BISanger
Estimate bisulfite conversion freqency from Sanger sequencing data
Cross-Rough-Atlantic-Projects
Blaster Projects
drtransformer
Heuristic cotranscriptional folding using the nearest neighbor energy model.
easyEvenOdd
The worst possible way to determine if an integer is even or odd in Python
klipper
Klipper is a 3d-printer firmware
laser-cutting
File repo for laser cutting designs
MCB-162-materials
Additional course materials for MCB 162 Fall 2022
PBEH1-figs
Figure plotting for PBEH1 data
PBEH2-amplicons
Scripts and sequences for generating amplicons used for sequence alignments
PBEH2-explo
Snakemake workflow for making diagnostic and initial analysis for PBEH2 Revio / Sequel II PacBio datasets
PBEH2-ZMW-vs-read-len
Plot ZMW hole number vs. read length for PacBio Revio sequencing dataset
peak-fold
Compare R-loop bisulfite conversion peaks to DNA folding predictions
pFC9RNAFoldingAtNicks
Using ViennaRNA folding prediction to look at predict RNA structure energetics at the site of Cas9 induced nicks from previous experiments
poloReleaseTesting
Ignore this repo. I am figuring out github actions stuff
rlooperVariableTopology
Rlooper on pFC8 and 53 under various topological densities
rpi-pico-print-monitor
Raspberry Pi Pico W based LED print status indicator
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
VR-insert-GHunter
Using GHunter program to predict G4 occurance in VR insert sequences
VRTransformer
Snakemake workflow that uses DrTransformer co-transcriptional RNA folding program to find alternative VR sequences