Church Lab

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 software

Deep_diversification_AAV

Bioinformatics code for paper associated with deep diversification of AAV

AAV_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 AMIs

crispr-images

Code for Shipman et al. 2017

Generative_AAV_design

Code and Data for Generative modeling for AAV design

optmage

Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)

agr_recoding

supporting code and data for Napolitano et al.

aws-utils

Docs and scripts for working with Amazon Web Services and compute tasks more generally

rlr

RLR (Schubert & Goodman et al.) - Documentation, Code, and Figures

aav_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".

churchlab.github.io

lac_repression

Code and processed data for Garruss et al. 2021 "Deep Representation Learning Improves Prediction of LacI-mediated Transcriptional Repression"

pydna

Python 3 classes for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut&paste cloning in Jupyter notebooks

PyVCF

A Variant Call Format reader for Python.

Vascularized-Organoids

Repository for Vascularized Organoids Paper

AAV2_library

Library of analysis for Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design

analyze_plate_reader_growth

Matlab script to analyze bacteria doubling time from plate reader data

C321evolve

Evolving a healthier recoded variant

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

dependence

Scripts and data analysis related to NSAA-dependence project

etfl

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

optimizing-complex-phenotypes

Supporting code for Kuznetsov, Goodman, Filsinger et al., 2017.

phip-stat

(DEVELOPMENT NOW AT lasersonlab) Analysis tools for PhIP-seq experiments

recoli57

Supporting code for Ostrov et al., Science, 2016

reference_genome_maker

Python scripts to create reference genome files (e.g. Genbank) from various inputs (e.g. vcf)

SEER

Code and data for SEER publication