jeffhsu3

octopi-research

BridgeRNADesigner

Software package to design bridge RNAs as described by Durrant & Perry et al.

Build-PMC-OA

chromax

Chromax is a breeding simulator based on JAX.

coco-annotator-ng

JsBroks COCO Annotator modernized

DAStk

Differential ATAC-seq toolkit

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

funsearch

gspread-pandas

A package to easily open an instance of a Google spreadsheet and interact with worksheets through Pandas DataFrames.

i-am-listening

long-form-factuality

Benchmarking long-form factuality in large language models. Original code for our paper "Long-form factuality in large language models."

m2stitch

MIST-inspired microscope image stitching package

megablocks

mesh-transformer-jax

Model parallel transformers in JAX and Haiku

nnUNet

nvidia-terraform-modules

Infrastructure as code for GPU accelerated managed Kubernetes clusters.

nvim-conda

Implementation of the conda package manager inside Neovim. Activate environments easily, update LSPs and more.

opentrons-python-api

Simple (and currently incomplete) Python wrapper around the Opentrons HTTP API

PDGrapher

Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks

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.

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

pylabrobot

A hardware agnostic interface and developer ecosystem for lab automation

Pyverilog

Python-based Hardware Design Processing Toolkit for Verilog HDL

scGPT

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

snakemake-storage-plugin-gcs

A Snakemake storage plugin for Google Cloud Storage

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

U-Mamba

U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation

weak-to-strong