EthanHolleman

ethanholleman.github.io

Source code for Ethan Holleman's personal website.

Rook-build

ADARColab

Repo for in vitro ADAR deamination of R-loops project related files

aquascope

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

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

race-to-insulin-assembly

RCWorkshop

rlooper-plasmids

rlooperVariableTopology

Rlooper on pFC8 and 53 under various topological densities

rpi-pico-print-monitor

Raspberry Pi Pico W based LED print status indicator

site_dev

This repo contains the markdown files, images, etc. that are used to render the html for my personal website using Hugo. You can visit the site at ethanholleman.com

snakeFeet

Snakemake workflow and scripts relating to read calling for Single Molecule R-loop footprinting (SMRF-seq).

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

wget

Stuff for wget-ing