To comprehensively evaluate the performance of GraphPCA and other competing algorithms, we generated a series of simulated data using scDesign3 [46]. With simulated datasets, one could use curated spatial domain labels as ground truth to evaluate the accuracy of the clustering results. Specifically,...
Set up the foreground and background colors. Print the generated graph paper. Firstly, open the Microsoft PowerPoint app and simply create a new presentation. Now, from the Home tab, go to the Slide > Layout drop-down option and choose the Blank option. Next, right-click on the blank sl...
All datasets used in this paper are available for download from the following websites. (1) Stereo-seq mouse olfactory bulb data: https://github.com/JinmiaoChenLab/SEDR_analyses. (2) Slide-seqV2 mouse olfactory bulb data: https://singlecell.broadinstitute.org/single_cell/study/SCP815/highly...
Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facili
existing spatial domain detection methods ignore the consistency of expression patterns and spatial arrangements between spots, as well as the severe gene dropout phenomenon present in srt data, resulting in suboptimal performance in identifying tissue spatial heterogeneity. results in this paper, we intro...
So in an issue paper, they started to abstract this into a mathematical problem. So the way they are doing this abstraction was to map the land into small dots — or what we call vertex — and the bridges will be abstracted as a line connecting them or the edge. So in terms of ...
In this paper, to solve the research problem presented in Section 3.2, we seek to find the answer to the main question: How can we use the CANN on graph structures to improve the performance of aspect-level SA? This question can be divided into the following four subquestions: (i) How...
paper [47]. Amino acids within the same group likely involve synonymous mutations due to their analogous characteristics. Then, each amino acid can be substituted by its category label and thus each protein is a string of integers. Next, a window of size three is used to slide across the ...
(Supplementary Fig.3). The input feature matrix X contains the gene expression of all cells in the sample and is of size N × D, where N is the number of cells and D is the number of genes. The input adjacency matrix AN x Nis binary in our paper, but can be weighted by a ...
region scRNA-seq data were obtained through GEO under accession numberGSE115746. The scRNA-seq and ST data of the human PDAC data were obtained through GEO under accession numberGSE111672. Source data for the main figures are provided with this paper.Source dataare provided with this paper. ...