Jeffrey Hsu's repositories
DAStk
Differential ATAC-seq toolkit
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
snakemake-storage-plugin-gcs
A Snakemake storage plugin for Google Cloud Storage
pylabrobot
A hardware agnostic interface and developer ecosystem for lab automation
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
long-form-factuality
Benchmarking long-form factuality in large language models. Original code for our paper "Long-form factuality in large language models."
opentrons-python-api
Simple (and currently incomplete) Python wrapper around the Opentrons HTTP API
chromax
Chromax is a breeding simulator based on JAX.
pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
pybrops
Python Breeding Optimizer and Simulator: A Python library for simulating and optimizing breeding pipelines.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
gspread-pandas
A package to easily open an instance of a Google spreadsheet and interact with worksheets through Pandas DataFrames.
coco-annotator-ng
JsBroks COCO Annotator modernized
U-Mamba
U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation
mesh-transformer-jax
Model parallel transformers in JAX and Haiku
m2stitch
MIST-inspired microscope image stitching package
PDGrapher
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
MEDIAR
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
vector-quantize-pytorch
Vector Quantization, in Pytorch
hlb-CIFAR10
Train to 94% on CIFAR-10 in <6.3 seconds on a single A100, the current world speed record. Or ~95.79% in ~110 seconds (or less!)
dash_router
A simple router for multi page Dash applications