spatial-transcriptomics 开源项目推荐（535 个）

seandavi /awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

jinworks /CellChat

R工具包，用于从单细胞和空间分辨转录组学中推断、可视化和分析细胞间通讯

scverse /squidpy

Spatial Single Cell Analysis in Python

smorabit /hdWGCNA

高维加权基因共表达网络分析

aristoteleo /PantheonOS

一个面向数据科学的通用、可演进且分布式的智能体框架与测试工具。

dmcable /spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Dana-Farber-AIOS /pathml

Tools for computational pathology

mahmoodlab /HEST

Integrating histology and spatial transcriptomics - NeurIPS 2024

OmicsML /dance

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

aristoteleo /spateo-release

Spatiotemporal modeling of spatial transcriptomics

scverse /decoupler

Python package to perform enrichment analysis from omics data.

prism-oncology /sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

jianhuupenn /SpaGCN

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

kharchenkolab /numbat

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

JianYang-Lab /gsMap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

kharchenkolab /Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

p-gueguen /Spatial_transcriptomics_tools

List of Spatial Transcriptomics related Tools organized per category

theMILOlab /SPATA2

A Toolbox for Spatial Transcriptomics Analysis

prism-oncology /novae

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

TianGzlab /OmicsClaw

Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper.