Code for running RFdiffusion

Coarse-graining of large single-cell RNA-seq data into metacells

Bioinformatics pipeline for single-cell 3' UTR isoform quantification

Bootstrapping methods for 3' UTR analysis of scRNA-seq

⚡ TabPFN: Foundation Model for Tabular Data ⚡

Bioinformatics tool for Locus Visualisation

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.

Efficient Differential Expression and Gene Aggregation for CRISPR screens.

A flexible and fast sgRNA counter from FASTQ Files

crispr screen visualization toolkit

Demultiplexing cell/nucleus hashing data for single-cell genomics

hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity

a python module for generate cell / guide matrices for demultiplex testing

🔬 BEDOPS: high-performance genomic feature operations

gia: Genomic Interval Arithmetic

bedtools-like functionality for interval sets in rust

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

This repo contains the codes and data for our Nature Communications paper: Deep learning resilience inference for complex networked systems.

C-GMVAE: Gaussian Mixture VAE with Contrastive Learning for Multi-Label Classification

Contrastive Variational Autoencoders

Text and code for the second edition of Think Bayes, by Allen Downey.

A PyTorch Library for Multi-Task Learning

Automated Explainable AI for Omics

Panoramic stitching of single cell data

Unifying Multimodal Variational Autoencoders (VAEs) in Pytorch