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Fig. 1 | Genome Biology

Fig. 1

From: Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

Fig. 1

Discrepancies between SVGs in a dataset annotated by six different packages. A Upset plots displaying the distinct intersections of SVGs identified in FF endometrial adenocarcinoma ovarian tissue dataset when analysed with SpaGCN, Squidpy, scGCO, Seurat, SPARK-X and SpatialDE. Bar chart in box displays the total number of SVGs identified by each package. B Pattern of expression of JCHAIN, a SVG identified by all six packages in FF endometrial adenocarcinoma ovarian tissue. Spots representing the capture regions of the Visium slide are overlayed on accompanying histological image. C Sorted q-values from SpatialDE results across the FF left ventricle datasets plotted against SPARK-X q-values for the same gene. D Gene ontology enrichment results from FF endometrial adenocarcinoma ovarian tissue dataset using SVGs identified by each package as inputs

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Genome Biology

ISSN: 1474-760X

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