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Terminal Bench for Science
Your Claude Code powered Linear agent that runs on any machine
🚧 Accepting Task Submissions 🚧
Dataloader for applying sequence models to personalized genomics
A simple yet versatile context engineered for scalable online data collection
Implementation of AlphaGenome, Deepmind's updated genomic attention model
Harbor is a framework for running agent evaluations and creating and using RL environments.
A benchmark for LLMs on complicated tasks in the terminal
Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
[ICLR'25] ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
The absolute trainer to light up AI agents.
[EMNLP2025] From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery
Causal discovery of gene regulatory programs from single-cell genomics
Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
The computational and statistical analyses of TenK10K phase 1 multiome data
Universal Single-Cell Genomics Preprocessing package
Decima is a Python library to train sequence models on single-cell RNA-seq data.
CHOIR : Clustering Hierarchy Optimization by Iterative Random forests (www.CHOIRclustering.com)
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.
ByteCheckpoint: An Unified Checkpointing Library for LFMs
CMD4 Plugin for Homebridge - Supports ~All Accessory Types & now all Characteristics too
A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
Biological sequence analysis for the modern age.
Simple, minimal implementation of the Mamba SSM in one file of PyTorch.