Popular GitHub Repositories for Transcriptomics

Tools for computational pathology

DANCE: a deep learning library and benchmark platform for single-cell analysis

Single cell perturbation prediction

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

空间转录组学人工智能代理绘制体内胰腺祖细胞成熟图谱

conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics

STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition

UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

Build foundation model on RNA or DNA data

Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data

Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"

MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics

MIRROR: Multi-Modal Pathological Self-Supervised Representation Learning via Modality Alignment and Retention

Generative models for transcriptomics profiles and proteins

An offical implementation of MEATRD: "MEATRD: Multimodal Anomalous Tissue Region Detection Enhanced with Spatial Transcriptomics." (AAAI 2025)

The spatial representation learning for spatial transcriptomics

Assessing the influence of training data composition on single-cell foundation model performance

Automated two-tiered pipeline for exploration of stress response pathways and transcriptomics in chemical risk assessment.

STFoundation: A Spatial Transcriptomic-based foundation model driven by expanding spatial transcriptomic and imaging datasets.