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Go 4 1 Updated Sep 3, 2024

Workflow Description Language (WDL) scripts for common vg workflows

WDL 19 9 Updated Oct 30, 2024

The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use th…

Jupyter Notebook 13,060 1,247 Updated Dec 12, 2024
Python 6 Updated Mar 23, 2022

A framework for creating grounded instruction based datasets and training conversational domain expert Large Language Models (LLMs).

Jupyter Notebook 343 41 Updated May 30, 2023

Ultima scripts related to downstream processing of WGS, MRD, methylation analysis

Jupyter Notebook 8 Updated Dec 9, 2024

UltimaGenomics repository for workflows compatible with AWS HealthOmics

WDL 11 3 Updated Nov 28, 2024
HTML 113 25 Updated Nov 8, 2024

A beautiful, simple, clean, and responsive Jekyll theme for academics

HTML 11,518 11,320 Updated Dec 12, 2024

Python-based preprocessing software for Illumina methylation arrays

Python 34 14 Updated Aug 17, 2023

Collection of notebook guides created by the Brev.dev team!

Jupyter Notebook 1,683 290 Updated Dec 12, 2024

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Python 52 3 Updated Dec 2, 2024

A minimal PyTorch re-implementation of the OpenAI GPT (Generative Pretrained Transformer) training

Python 20,363 2,537 Updated Aug 15, 2024
Python 12 3 Updated May 24, 2022

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

Assembly 613 85 Updated Jun 15, 2024

Training code for CI-SpliceAI

Python 1 Updated Jun 3, 2022
TypeScript 747 100 Updated Jan 2, 2024

Code for the emrQA question answering dataset

Python 144 36 Updated Feb 9, 2022

The next version of bwa-mem

C++ 2 Updated Jul 5, 2023

Generating and Imputing Tabular Data via Diffusion and Flow XGBoost Models

Python 144 13 Updated Aug 6, 2024

Platform to experiment with the AI Software Engineer. Terminal based. NOTE: Very different from https://gptengineer.app

Python 52,636 6,844 Updated Nov 17, 2024

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

148 15 Updated Dec 4, 2024

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

C 16 3 Updated Jun 22, 2023

Enhanced ChatGPT Clone: Features Agents, Anthropic, AWS, OpenAI, Assistants API, Azure, Groq, o1, GPT-4o, Mistral, OpenRouter, Vertex AI, Gemini, Artifacts, AI model switching, message search, Code…

TypeScript 19,774 3,300 Updated Dec 14, 2024

Classifying tumor types based on Whole Genome Sequencing (WGS) data

Python 4 Updated Oct 7, 2021
C++ 1 Updated Oct 14, 2022

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Python 10 Updated Feb 4, 2024

The ChatGPT Retrieval Plugin lets you easily find personal or work documents by asking questions in natural language.

Python 21,092 3,682 Updated Jul 4, 2024

Clinical sequencing-based primary site classifier

Jupyter Notebook 34 9 Updated Jul 12, 2024
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