churchlab/millstone

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47
Rank 600,971 (Top 12 %)
Language
Python
License
MIT License
Created about 11 years ago
Updated over 2 years ago

churchlab/millstone

churchlab

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Genome engineering and analysis software

UniRep

UniRep model, usage, and examples.

UniRep-analysis

Analysis and figure code from Alley et al. 2019.

Jupyter Notebook

low-N-protein-engineering

Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".

Jupyter Notebook

Deep_diversification_AAV

Bioinformatics code for paper associated with deep diversification of AAV

Jupyter Notebook

AAV_fitness_landscape

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

Jupyter Notebook

ml-ami-builder

Packer scripts to build nvidia-enabled AMIs

crispr-images

Code for Shipman et al. 2017

vdj

python package for working with immune receptor sequence data

Generative_AAV_design

Code and Data for Generative modeling for AAV design

Jupyter Notebook

optmage

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

rlr

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

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

churchlab.github.io

ulutil

Python utilities for Church lab work (mostly DNA sequencing-related)

Vascularized-Organoids

Repository for Vascularized Organoids Paper

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".

Jupyter Notebook

lac_repression

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