Python package providing API and CLI access to recount3

Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.

code to run Otari and obtain Otari predictions

personal genome constructor

Personal diploid genome creation and coordinate conversion

Firth penalized models in Python

AlphaGenome PyTorch port

A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription

Multi-Omics Factor Analysis

High accuracy RAG for answering questions from scientific documents with citations

Multi-omics factor analysis v2

Research code accompanying AlphaGenome

Modify genomes based on VCF

This repo contains a nextflow pipeline to do colocalisation analysis of QTLs against GWASs

Convert various sequence formats to FASTA

an API for intersections of genomic data

Ultra-fast variant effect prediction using first order and second order PWMs

Awesome resources on normalizing flows.

Normalizing flows in PyTorch

Biological foundation models

A generative model for programmable protein design

Ultrafast method to compute single-sample gene set enrichment scores for gene expression or proteomics data

A Collection of Variational Autoencoders (VAE) in PyTorch.

Simple and clean implementation of Conditional Variational AutoEncoder (cVAE) using PyTorch

A guided tour on how to use HuggingFace large language models on Macs with Apple Silicon

Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction

Python Client Library for the G2P Portal API

FRASER - Find RAre Splicing Events in RNA-seq