BenchmarkST

We present a comprehensive evaluation of the performance of state-of-the-art methods for cell/spot clustering, alignment, and integration on spatial transcriptomic datasets. Our goal is to provide the research field with a fair evaluation and comparison of all available methods to facilitate the users’ choice as well as shed more light on further developments to focus on the challenging aspects of ST based tasks.

Table of Content

• Online Documentation
• Installation
• Repository Description
• General Usage
  • Original Github Repository Links and Our Script for Clustering Task
    • BANKSY
    • ADEPT
    • GraphST
    • SpaceFLow
    • conST
    • ConGI
    • SpatialPCA
    • DR-SC
    • STAGATE
    • CCST
    • SEDR
    • SpaGCN
    • DeepST
    • BayesSpace
    • BASS
    • PRECAST
  • Original Github Repository Links and Our Script for Alignment Task
    • STAlign
    • GPSA
    • PASTE
    • PASTE2
    • SPACEL
  • Original Github Repository Links and Our Script for Integration Task
    • SPIRAL
    • STAligner
    • PRECAST
    • BASS
    • DeepST
• Citation

Online documentation&tutorials

We hope the online readthedocs.io version of doc of our project BenchmarkST would make things easier and more organized. Feel free to navigate to it through the following link.

Online Doc: Here

Installation

We strongly suggest to follow the installation instructions given by each method. We will also provide the .yaml file of our debugging environment in each subfolder.

Repository description

We provide all the jupyter notebooks in each subfolder to run and evaluate all algorithms for all datasets with ground truth annotation, and to reproduce the results introduced in our paper.

General Usage

Please follow the readme or jupyter notebook instructions in each subfolder for further details.

original Github repository links and our script for Clustering task:

BANKSY

Github link:https://github.com/prabhakarlab/Banksy

Our tutorial: run_BANKSY

ADEPT

Github link: https://github.com/maiziezhoulab/ADEPT

Our tutorial: run_ADEPT

GraphST

Github link: https://github.com/JinmiaoChenLab/GraphST

Our tutorial: run_GraphST

SpaceFLow

Github link: https://github.com/hongleir/SpaceFlow

Our tutorial: run_SpaceFLow

conST

Github link: https://github.com/ys-zong/conST

Our tutorial: run_conST

ConGI

Github link: https://github.com/biomed-AI/ConGI

Our tutorial: run_conGI

SpatialPCA

Github link: https://github.com/shangll123/SpatialPCA

Our tutorial: run_SpatialPCA

DR-SC

Github link: https://github.com/feiyoung/DR.SC

Our tutorial: run_DRSC

STAGATE

Github link: https://github.com/QIFEIDKN/STAGATE_pyG

Our tutorial: run_STAGATE

CCST

Github link: https://github.com/xiaoyeye/CCST

Our tutorial: run_CCST

SEDR

Github link: https://github.com/JinmiaoChenLab/SEDR

Our tutorial: run_SEDR

SpaGCN

Github link: https://github.com/jianhuupenn/SpaGCN

Our tutorial: run_SpaGCN

DeepST

Github link: https://github.com/JiangBioLab/DeepST

Our tutorial: run_DeepST

BayesSpace

Github link: https://github.com/edward130603/BayesSpace

Our tutorial: run_BayesSpace

BASS

Github link: https://github.com/zhengli09/BASS

Our tutorial: run_BASS

PRECAST

Github link: https://github.com/cran/PRECAST

Our tutorial: run_PRECAST

original Github repository links and our script for Alignment task:

STAlign

Github link: https://github.com/JEFworks-Lab/STalign

Our tutorial: run_STAlign

GPSA

Github link: https://github.com/andrewcharlesjones/spatial-alignment

Our tutorial: run_GPSA

PASTE

Github link: https://github.com/raphael-group/paste

Our tutorial: run_PASTE

PASTE2

Github link: https://github.com/raphael-group/paste2

Our tutorial: run_PASTE2

SPACEL

Github link: https://github.com/QuKunLab/SPACEL

Our tutorial: run_SPACEL

original Github repository links and our script for Integration task:

SPIRAL

Github link: https://github.com/guott15/SPIRAL

Our tutorial: run_SPIRAL

STAligner

Github link: https://github.com/zhanglabtools/STAligner

Our tutorial: run_STAligner

PRECAST

Github link: https://github.com/cran/PRECAST

Our tutorial: run_PRECAST

BASS

Github link: https://github.com/zhengli09/BASS

Our tutorial: run_BASS

DeepST

Github link: https://github.com/JiangBioLab/DeepST

Our tutorial: run_DeepST

Citation

Hu Y, Xie M, Li Y, Rao M, Shen W, Luo C, Qin H, Baek J, Zhou XM. Benchmarking clustering, alignment, and integration methods for spatial transcriptomics. Genome Biol. 2024 Aug 9;25(1):212. PubMed Central PMCID: PMC11312151.