Decima is a Python library to train sequence models on single-cell RNA-seq data.

Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.

UCE is a zero-shot foundation model for single-cell gene expression data

A high-performance Python-based I/O system for large (and small) deep learning problems, with strong support for PyTorch.

Analysis scripts used for the manuscript Benchmarking deep learning splice prediction tools using functional splice assays

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

A template for standard compliant snakemake-workflows

Implementing a ChatGPT-like LLM in PyTorch from scratch, step by step

https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2

Benchmarking splice variant prediction algorithms using massively parallel splicing assays

Code to run analysis in "A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions"

CADD scripts release for offline scoring. For more information about CADD, please visit our website

TorchMultimodal is a PyTorch library for training state-of-the-art multimodal multi-task models at scale.

Implementation of "Autoencoding beyond pixels using a learned similarity metric" using Pytorch

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical…

Collection of generative models in Pytorch version.

Unofficial trade republic API

Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics

Toolset for training quantitative sequence to function models.

TGVAE: Transformer Graph Variational Autoencoder

Implementation of Graph Transformer in Pytorch, for potential use in replicating Alphafold2

Pipeline for efficient genomic data processing.

Demonstrations of Loss of Plasticity and Implementation of Continual Backpropagation