voyageR

A benchmark of computational methods for spatial gene expression.

Index

• Useful Links
• Packages by Category
  • Cell Type Deconvolution
  • Spatially Variable Genes
  • Spatial Region
  • Gene Patterns
  • Cell-Cell Interactions
• Datasets
• Benchmarking Metrics

Useful Links

Link
SpatialDB: a database for spatially resolved transcriptomes
Awesome-Spatial-Omics: repository for collecting single-cell spatial omics resources
10x Visium Datasets
t-CyCIF Datasets
Giotto Datasets
Spatial Transcriptomics Datasets
Paper: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
Paper

Packages by Category

Cell Type Deconvolution

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Package	Language	Paper	Repo
NMFreg	Python; Matlab	paper	https://github.com/tudaga/NMFreg_tutorial
Seurat3	R	paper	https://satijalab.org/seurat/
RCTD	R	paper	https://github.com/dmcable/RCTD
Tangram	Python	paper	https://github.com/broadinstitute/Tangram
stereoscope	Python	paper	https://github.com/almaan/stereoscope
DSTG	Python	paper	https://github.com/Su-informatics-lab/DSTG
SPOTlight	R	paper	Repo: https://github.com/MarcElosua/SPOTlight Analisi: https://github.com/MarcElosua/SPOTlight_deconvolution_analysis
Giotto	R	paper	https://rubd.github.io/Giotto_site/
CellDART	Python	paper	https://github.com/mexchy1000/CellDART
Spacell	Python	paper	https://github.com/BiomedicalMachineLearning/Spacell
SpiceMix	Python	paper	https://github.com/ma-compbio/SpiceMix
SpatialDWLS	R	paper	https://github.com/rdong08/spatialDWLS_dataset
Squidpy	Python	paper	Repo: https://github.com/theislab/squidpy Doc: https://squidpy.readthedocs.io/en/latest/
STdeconvolve	R	paper	https://github.com/JEFworks-Lab/STdeconvolve

Spatially Variable Genes

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Package	Language	Paper	Repo
trendsceek	R	paper	https://github.com/edsgard/trendsceek
SpatialDE	Python	paper	https://github.com/Teichlab/SpatialDE
scGCO	Python	paper	https://github.com/WangPeng-Lab/scGCO
Seurat3	R	paper	https://satijalab.org/seurat/
RayleighSelection	R; C++	paper	https://github.com/CamaraLab/RayleighSelection
SPARK	R; C++	paper	https://github.com/xzhoulab/SPARK
GPcounts	Python	paper	https://github.com/ManchesterBioinference/GPcounts
GLISS	NA	paper	https://github.com/junjiezhujason/gliss
singleCellHaystack	R	paper	Github: https://github.com/alexisvdb/singleCellHaystack CRAN: https://cran.r-project.org/web/packages/singleCellHaystack/index.html
SPATA	R	paper	Repo: https://github.com/theMILOlab/SPATA Sito: https://themilolab.github.io/SPATA/
Giotto	R	paper	Repo: https://github.com/RubD/Giotto DevelVersion: https://rubd.github.io/Giotto_site/ Sito: http://spatialgiotto.rc.fas.harvard.edu/
SOMDE	Python	paper	https://github.com/WhirlFirst/somde
Splotch	Python (e R)	paper	https://github.com/tare/Splotch
SpaGCN	Python	paper	https://github.com/jianhuupenn/SpaGCN
BOOST-GP	C++; R	Published paper Preprint from arXiv	https://github.com/Minzhe/BOOST-GP
Gene-Spatial	Python	paper	https://github.com/RuishanLiu/Gene-Spatial
STUtility	R	paper	Repo: https://github.com/jbergenstrahle/STUtility Doc: https://ludvigla.github.io/STUtility_web_site/index.html
JSTA	Python	paper	https://github.com/wollmanlab/JSTA
Spark-X	R	paper	https://github.com/xzhoulab/SPARK
MERINGUE	R	paper	https://github.com/JEFworks-Lab/MERINGUE
Squidpy	Python	papers	https://squidpy.readthedocs.io/en/stable/index.html
nnSVG	R		https://github.com/lmweber/nnSVG

Spatial Region

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Package	Language	Paper	Repo
smfishHmrf	python; C++	paper	https://bitbucket.org/qzhudfci/smfishhmrf-py/src/master/ - https://bitbucket.org/qzhudfci/smfishhmrf-r/src/master/
SSAM	Python; C++	paper	https://github.com/HiDiHlabs/ssam
stLearn	Python	paper	Repo: https://github.com/BiomedicalMachineLearning/stLearn/ Docs: https://stlearn.readthedocs.io/en/latest/
BayesSpace	R; C++	paper	https://github.com/edward130603/BayesSpace
Baysor	Julia	paper	https://github.com/kharchenkolab/Baysor
SpaGCN	Python	paper	https://github.com/jianhuupenn/SpaGCN
MULTILAYER	Python	paper	https://github.com/SysFate/MULTILAYER
Spage2vec	Python	paper	https://github.com/wahlby-lab/spage2vec

Gene Patterns

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Package	Language	Paper	Repo
SpatialDE	Python	paper	https://github.com/Teichlab/SpatialDE
std-nb	C++	paper	https://github.com/SpatialTranscriptomicsResearch/std-nb
stLearn	Python	paper	Repo: https://github.com/BiomedicalMachineLearning/stLearn/ Docs: https://stlearn.readthedocs.io/en/latest/
GLISS	NA	paper
sepal	Python	paper	https://github.com/almaan/sepal
MERINGUE	R	paper	https://github.com/JEFworks-Lab/MERINGUE

Cell-Cell Interactions

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Package	Language	Paper	Repo
SVCA	R; Python; C; C++; Fortran	paper	https://github.com/damienArnol/svca
SpaOTsc	Python	paper	https://github.com/zcang/SpaOTsc
MISTy	R	paper	Repo: https://github.com/saezlab/mistyR/ Sito: https://saezlab.github.io/misty/
stLearn	Python	paper	Repo: https://github.com/BiomedicalMachineLearning/stLearn/ Docs: https://stlearn.readthedocs.io/en/latest/
DIALOGUE	R	paper	https://github.com/livnatje/DIALOGUE
GCNG	Python	paper	https://github.com/xiaoyeye/GCNG
Giotto	R	paper	Repo: https://github.com/RubD/Giotto DevelVersion: https://rubd.github.io/Giotto_site/ Sito: http://spatialgiotto.rc.fas.harvard.edu/
MERINGUE	R	paper	https://github.com/JEFworks-Lab/MERINGUE

Datasets

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Name/Tissue	Version	Technology	Paper	Download link	Used by	Ground Truth (if present)	Accessibility	Notes
human postmortem DLPFC tissue sections from two pairs of ‘spatial replicates’ from three independent neurotypical adult donors		10x Visium	spatialLIBD data paper	SpatialLIBD			Tutorial	The package provides also some datasets in SpE format
Mouse somatosensory cortex		seqFISH+	paper	directory	Giotto
Mouse olfactory bulb		seqFISH+	paper	directory
Mouse brain cerebellum		Slide-Seq	paper	original link directory
Mouse brain cortex		StarMAP 3D	paper	original link directory
Mouse somatosensory cortex		osmFISH	paper	original link directory
Mouse preoptic hypothalamus		merFISH 3D	paper	original link directory
Mouse spleen		CODEX	paper	directory
Human pancreatic ductal adenocarcinoma (PDAC)		tissue-based cyclic immunofluorescence (t-CyCIF)	paper	original link directory				Different datasets
triple negative breast cancer (TNBC) patients		MIBI	paper	original link directory
Mouse olfactory bulb		Spatial Transcriptomics	paper	original link directory
Human breast cancer		Spatial Transcriptomics	paper	original link
Mouse hippocampus		seqFISH	paper	Download from supplementary material	SpatialDE
Human osteosarcoma cell line		MERFISH	paper	From the Zhuang lab website they downloaded this file MERFISH .zip	SpatialDE
Xenopus embryos		Frog Development RNA-seq data	paper	Download GSE65785	SpatialDE
Mouse gastrulation epiblast cells from mice at age embryonic day 6.5		scRNA-seq	paper	Download link	trendsceek			we investigated whether trendsceek could find spatial patterns in two-dimensional representations of dissociated single-cell data (t-SNE).
Human developmental heart		ST	paper	Download	SpatialDWLS (ST and scRNA-seq)			ST and scRNA-seq
Adult Mouse Brain Section (Visium and scRNA-seq)	v1.1.0	10x Visium e scRNA-seq	paper scRNA-seq	Download Spatial 10x Visium - Download scRNA-seq	SpatialDWLS (Spatial and scRNA-seq)			Annotated data here for the scRNA-seq
MOp: Primary motor area of health adult mouse brainc	v3	10Xv3 scRNA-seq and Slide-seq2 (Spatial; Adult mouse brain)	paper	Download scRNA-seq - Download Slide-seq2 (Spatial) - Download markers genes	Tangram			Marker genes obtained from here; All datasets need to be unzipped: resulting h5ad and csv files should be placed in the data folder. Link obtained from their tutorial
Mouse lumbar spinal cord (presymptomatic)		ST	paper	Avalaible here
Postmortem lumbar spinal cord SLA		ST	paper	Avalaible here
Postmortem cervical spinal cord SLA		ST	paper	Avalaible here
Human Melanoma lymph node biopsies		ST	paper	Spatial Research Download
Human Prostate Cancer		ST	paper	Spatial Research Download
Human periodontal tissue		ST	paper
Adult human health tissue		ST	paper	Spatial Research Download
Model Plant Species		ST	paper	Spatial Research Download

Benchmarking Metrics

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Package	Language	Category	Analysis	Metric