Pinned Repositories
autopy
A simple, cross-platform GUI automation toolkit for Python.
biodas
A django tastypie implementation of a BioDAS server.
biopython
Official git repository for Biopython (converted from CVS)
bioruby-ngs
This plugins is intended to wrap the common software used for Next Generation Sequencing data
combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
d3py
a plottling library for python, based on D3
dalliance
Interactive web-based genome browser.
edgepy
python based edgeR for learning and fun
genda
genda a genetics library in pandas
mimRNA
Useful functions to use with edgeR
jeffhsu3's Repositories
jeffhsu3/octopi-research
jeffhsu3/bioconda-recipes
Conda recipes for the bioconda channel.
jeffhsu3/BridgeRNADesigner
Software package to design bridge RNAs as described by Durrant & Perry et al.
jeffhsu3/Build-PMC-OA
jeffhsu3/chromax
Chromax is a breeding simulator based on JAX.
jeffhsu3/DAStk
Differential ATAC-seq toolkit
jeffhsu3/dspy_reasoning
jeffhsu3/entropix
Entropy Based Sampling and Parallel CoT Decoding
jeffhsu3/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
jeffhsu3/formulaic-contrasts
Build contrasts for models defined with formulaic
jeffhsu3/i-am-listening
jeffhsu3/long-form-factuality
Benchmarking long-form factuality in large language models. Original code for our paper "Long-form factuality in large language models."
jeffhsu3/Marco-o1
An Open Large Reasoning Model for Real-World Solutions
jeffhsu3/nnUNet
jeffhsu3/nvidia-terraform-modules
Infrastructure as code for GPU accelerated managed Kubernetes clusters.
jeffhsu3/OpenHands
🙌 OpenHands: Code Less, Make More
jeffhsu3/OpenMDAO
OpenMDAO repository.
jeffhsu3/opentrons-python-api
Simple (and currently incomplete) Python wrapper around the Opentrons HTTP API
jeffhsu3/PRIME
jeffhsu3/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
jeffhsu3/pybrops
Python Breeding Optimizer and Simulator: A Python library for simulating and optimizing breeding pipelines.
jeffhsu3/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
jeffhsu3/pylabrobot
A hardware agnostic interface and developer ecosystem for lab automation
jeffhsu3/Pyverilog
Python-based Hardware Design Processing Toolkit for Verilog HDL
jeffhsu3/snakemake-storage-plugin-gcs
A Snakemake storage plugin for Google Cloud Storage
jeffhsu3/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
jeffhsu3/snipar
Imputation of parental genotypes, inference of sibling IBD segments, family based GWAS, and polygenic score analyses.
jeffhsu3/SWE-Gym
jeffhsu3/tabby
Self-hosted AI coding assistant
jeffhsu3/unitree_rl_gym