A benchmark of computational methods for spatial gene expression.
- Useful Links
- Packages by Category
- Datasets
- Benchmarking Metrics
Package | Language | Paper | Repo |
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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 |
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 |
Package | Language | Paper | Repo |
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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 |
Name/Tissue | Version | Technology | Paper | Download link | Used by | Ground Truth (if present) | Accessibility | Notes |
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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 |
Package | Language | Category | Analysis | Metric |
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