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Starred repositories

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Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.

Python 36 5 Updated Jan 17, 2025
Shell 9 1 Updated Jan 7, 2025

Agent framework for constructing language model agents and training on constructive tasks.

Python 63 9 Updated Feb 18, 2025

Gymnasium framework for training language model agents on constructive tasks

Python 143 18 Updated Feb 19, 2025

Get up and running with Llama 3.3, DeepSeek-R1, Phi-4, Gemma 2, and other large language models.

Go 127,592 10,385 Updated Feb 19, 2025

High accuracy RAG for answering questions from scientific documents with citations

Python 6,954 687 Updated Feb 19, 2025

Work in progress transmit from Google Code

Java 1,114 288 Updated Jan 3, 2018

Implementation of paper - YOLOv7: Trainable bag-of-freebies sets new state-of-the-art for real-time object detectors

Jupyter Notebook 13,593 4,271 Updated Aug 19, 2024

Particle dynamics and simulated annealing for chromosome structure calculation

Python 28 11 Updated Mar 15, 2024

ORB forcefield models from Orbital Materials

Python 287 38 Updated Feb 6, 2025

Official repository for the Boltz-1 biomolecular interaction model

Python 1,591 211 Updated Feb 19, 2025

A toolkit for QC and visualization of ATAC-seq results.

C++ 67 10 Updated Jan 8, 2025

Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence

C++ 2 2 Updated Feb 10, 2025

Source code for RNA-FrameFlow: SE(3) Flow Matching for 3D RNA Backbone Design

Python 38 6 Updated Jan 4, 2025

Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).

Python 31 8 Updated Feb 17, 2022

Tools for fiberseq data written in rust.

Rust 44 6 Updated Feb 17, 2025

Quick pre-QC knee plots for barcode based scRNAseq data

C++ 12 Updated Dec 8, 2018
Python 1,706 195 Updated Jan 16, 2025

Software for the visualization of sequence-function relationships

Jupyter Notebook 193 39 Updated Jan 31, 2025

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Nim 723 101 Updated Jan 17, 2025

👁️ Python library to plot DNA sequence features (e.g. from Genbank files)

Python 613 93 Updated Jan 9, 2025

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Python 460 87 Updated Oct 9, 2024

LLM training in simple, raw C/CUDA

Cuda 25,653 2,951 Updated Oct 2, 2024

A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.

Python 18 4 Updated Jan 7, 2025

Script to automatically create and run IGV snapshot batchscripts

Python 140 50 Updated Jan 13, 2023

Aggregate results from bioinformatics analyses across many samples into a single report.

JavaScript 1,267 612 Updated Feb 9, 2025

ATAC-seq peak-calling and QC analysis pipeline

Nextflow 197 125 Updated Feb 12, 2025

A bioinformatics tool for working with modified bases

Rust 171 8 Updated Jan 30, 2025

Chromatin interaction aware gene regulatory modeling with graph attention networks

Python 24 3 Updated Feb 21, 2023
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