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UniRep
UniRep model, usage, and examples.UniRep-analysis
Analysis and figure code from Alley et al. 2019.low-N-protein-engineering
Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".millstone
Genome engineering and analysis softwareDeep_diversification_AAV
Bioinformatics code for paper associated with deep diversification of AAVAAV_fitness_landscape
Analysis for "Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design"ml-ami-builder
Packer scripts to build nvidia-enabled AMIscrispr-images
Code for Shipman et al. 2017vdj
python package for working with immune receptor sequence dataoptmage
Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)rlr
RLR (Schubert & Goodman et al.) - Documentation, Code, and Figuresagr_recoding
supporting code and data for Napolitano et al.aws-utils
Docs and scripts for working with Amazon Web Services and compute tasks more generallychurchlab.github.io
ulutil
Python utilities for Church lab work (mostly DNA sequencing-related)Vascularized-Organoids
Repository for Vascularized Organoids Paperaav_rep_scan
Contains code used to generate oligonucleotides for AAV2 rep scanning saturation mutagenesis library and to analyze resulting NGS data. Also includes code used to generate all figures in "Comprehensive mutagenesis maps the effect of all single codon mutations in the AAV2 rep gene on AAV production".lac_repression
Code and processed data for Garruss et al. 2021 "Deep Representation Learning Improves Prediction of LacI-mediated Transcriptional Repression"Love Open Source and this site? Check out how you can help us