A cross-platform proteomics data analysis suite

Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.

Genome modeling and design across all domains of life

Temporal Kolmogorov-Arnold Transformer

Examples for gget (https://github.com/pachterlab/gget).

Embeddable genomic visualization component based on the Integrative Genomics Viewer

Module for embedding igv.js in an IPython notebook

A command-line tool to mitigate homology-based data leakage in sequence-to-expression models

Making Protein folding accessible to all!

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Official repository for the ProteinGym benchmarks

Muon optimizer: +>30% sample efficiency with <3% wallclock overhead

MACS -- Model-based Analysis of ChIP-Seq

deep learning-inspired explainable sequence model for transcription initiation

A Python library for fast and easy access to genomic resources such as sequence, data tracks, and annotations

Genomic Pre-trained Network

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

Official implementation for ProtHyena, a fast and efficient protein language model

Benchmarks for classification of genomic sequences

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

The most recent documentation of OpenReview

RNA-seq prediction with deep convolutional neural networks.

Repository for StripedHyena, a state-of-the-art beyond Transformer architecture

Snakemake workflow management system and CLI generation tool

Repository documenting applications of the ML4GLand suite on published datasets

A set of tutorials for how to use all the tools in ML4GLand

Interpreting sequence-to-function machine learning models