LIANA+: an all-in-one framework for cell-cell communication

R package implementation of Milo for testing for differential abundance in KNN graphs

make 'ggplot' graphics interactive

Multi-Omics Factor Analysis

scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

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A virtual lab of LLM agents for science research

Arc Virtual Cell Atlas

State is a machine learning model that predicts cellular perturbation response across diverse contexts

[NeurIPS 2024] BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

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

Modeling complex perturbations with CellFlow

AUCell: score single cells with gene regulatory networks

A Python-based compendium of GPU-optimized aging clocks.

CpGPT: a Foundation Model for DNA Methylation.

JAX-based neural network library

Flax is a neural network library for JAX that is designed for flexibility.

Foundation Models for Genomics & Transcriptomics

Tissue-Gene Fine-Mapping

Cell age determination by scATAC-seq and bulk-ATAC-seq

Dynamics analysis of Alternative PolyAdenylation from RNA-seq

DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)

polyApipe

Methods to discover gene programs on single-cell data

An implement R package to visualize GSEA results

Spatial transcriptomics of heart tissue

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Genome modeling and design across all domains of life