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aav2_library

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

aav_fitness_landscape

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

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".

agr_recoding

supporting code and data for Napolitano et al.

analyze_plate_reader_growth

Matlab script to analyze bacteria doubling time from plate reader data

aws-utils

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

biopython

Official git repository for Biopython (converted from CVS)

c321evolve

Evolving a healthier recoded variant

churchlab.github.io

cloudbiolinux

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

crispr-images

Code for Shipman et al. 2017

deep_diversification_aav

Bioinformatics code for paper associated with deep diversification of AAV

dependence

Scripts and data analysis related to NSAA-dependence project

django-celery-testworker

Test functions to use with Django for tests that depend on the execution of Celery tasks

django-jenkins

Plug and play continuous integration with django and jenkins

ecoli-sequence-conservation

Representation for per-base conservation among various E. coli strains

etfl

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

generative_aav_design

Code and Data for Generative modeling for AAV design

jbrowse

Modern JavaScript-based Genome Browser

lac_repression

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

low-n-protein-engineering

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

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

millstone

Genome engineering and analysis software

ml-ami-builder

Packer scripts to build nvidia-enabled AMIs

nnn_sequencing_scripts

Python scripts used to analyze the NNN Illumina sequencing data

optimizing-complex-phenotypes

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

optmage

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

phip-stat

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

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.