Pinned Repositories
casanger
Snakemake workflow for visualization of Cas9 nickase validation via Sanger sequencing
ethanholleman.github.io
Source code for Ethan Holleman's personal website.
fridge_master_2000
Making my old fridge smarter with raspberry pi zero and some sensors
ImageToBlink
Possibly the world's worst image encoder. Convert any image to a micropython program (tested on RPi Pico) that will use the onboard LED to blink hexidecimal image data via morse code.
leafly_scraper
Scripts for scraping and visualizing leafly.com strain data
plasmid-VR-design
Snakemake wrapped Python and R based workflow for generating and visualizing nucleotide regions with systematic variation in GC / AT skew and GC / AT content with or without clustering for R-loop formation investigation.
pyCaliLegi
Automate pulling basic information about California legislation using Python and the Selenium package.
RDBC
Rosetta ligand docking batch job submission control and organizer
rlooper
R-loop equilibrium energetic modeling and prediction software
Marco_Polo
Polo is a python GUI build using the PyQt library for high-throughput crystallization screening users. Created by Ethan Holleman for the 2020 BioXFEL summer internship program. Funding provided through NSF BioXFEL STC Grant Number 1231306, NSF BIO 2029943, NIH NIGMS 124135.
EthanHolleman's Repositories
EthanHolleman/ethanholleman.github.io
Source code for Ethan Holleman's personal website.
EthanHolleman/Rook-build
EthanHolleman/ADARColab
Repo for in vitro ADAR deamination of R-loops project related files
EthanHolleman/aquascope
EthanHolleman/BISanger
Estimate bisulfite conversion freqency from Sanger sequencing data
EthanHolleman/Cross-Rough-Atlantic-Projects
Blaster Projects
EthanHolleman/drtransformer
Heuristic cotranscriptional folding using the nearest neighbor energy model.
EthanHolleman/easyEvenOdd
The worst possible way to determine if an integer is even or odd in Python
EthanHolleman/klipper
Klipper is a 3d-printer firmware
EthanHolleman/laser-cutting
File repo for laser cutting designs
EthanHolleman/MCB-162-materials
Additional course materials for MCB 162 Fall 2022
EthanHolleman/PBEH1
EthanHolleman/PBEH1-figs
Figure plotting for PBEH1 data
EthanHolleman/PBEH2-amplicons
Scripts and sequences for generating amplicons used for sequence alignments
EthanHolleman/PBEH2-explo
Snakemake workflow for making diagnostic and initial analysis for PBEH2 Revio / Sequel II PacBio datasets
EthanHolleman/PBEH2-ZMW-vs-read-len
Plot ZMW hole number vs. read length for PacBio Revio sequencing dataset
EthanHolleman/peak-fold
Compare R-loop bisulfite conversion peaks to DNA folding predictions
EthanHolleman/pFC9RNAFoldingAtNicks
Using ViennaRNA folding prediction to look at predict RNA structure energetics at the site of Cas9 induced nicks from previous experiments
EthanHolleman/poloReleaseTesting
Ignore this repo. I am figuring out github actions stuff
EthanHolleman/race-to-insulin-assembly
EthanHolleman/RCWorkshop
EthanHolleman/rlooper-plasmids
EthanHolleman/rlooperVariableTopology
Rlooper on pFC8 and 53 under various topological densities
EthanHolleman/rpi-pico-print-monitor
Raspberry Pi Pico W based LED print status indicator
EthanHolleman/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
EthanHolleman/snakeFeet
Snakemake workflow and scripts relating to read calling for Single Molecule R-loop footprinting (SMRF-seq).
EthanHolleman/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
EthanHolleman/VR-insert-GHunter
Using GHunter program to predict G4 occurance in VR insert sequences
EthanHolleman/VRTransformer
Snakemake workflow that uses DrTransformer co-transcriptional RNA folding program to find alternative VR sequences
EthanHolleman/wget
Stuff for wget-ing