Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial informat...
The list of the Seurat marker genes in all cell clusters is provided in Supplementary Table S3. (C) Gene ontology (GO) enrichment analysis for biological processes only (marker genes with minimum AUC = 0.7, and GO terms supported by ≥ 2 genes), for top marker genes in each ind...
Now genesets showing overlap with the marker ligands and receptors are stored intumor.obj@pathway[['pathwayLR']]. Then we score the pathways to measure the activation levels for each pathway in each cell. # To compute pathway activation score by the gsva algorithm or in an average manner #...
The “DotPlot” function was then used to visualize the expression level of marker genes in a single cluster [20]. These clusters are assigned to known cell lineages by marker genes. Clusters of cells are identified using the K-nearest neighbor (KNN) algorithm and the “FindClusters” ...
However, as our algorithm is designed for disjoint accesses, it performs significantly better on systems with high concurrency and non-uniform memory architecture. In addition, the proposed solution also implements a general doubly linked list, the first lock-free implementation that only needs the ...
Mesh decimation begins with the configuration of aDecimator. Besides setting parameters to select the error metric or the stopping criterion this also includes the selection of the mesh to process. This configuration prepares the decimation queue for the main algorithm by evaluating all edges of the...
Space-adaptive lock-free free-list using pointer-s 优质文献 相似文献 参考文献 引证文献Fast and Efficient Graph Traversal Algorithm for CPUs: Maximizing Single-Node Efficiency Graph-based structures are being increasingly used to model data and relations among data in a number of fields. Graph-based...
2c). In this paper, we use two network control-based methods, i.e., minimum feedback vertex sets (MFVS)32 and minimum dominating sets (MDS)34, to obtain the driver gene candidates (Fig. 2c and Methods). Since controlling a whole network usually requires a number of driver nodes24, ...
Finally, CytoSPACE assigns each cell to spatial coordinates in a manner that minimizes a correlation-based cost function constrained by the inferred number of cells per spot via a shortest augmenting path optimization algorithm. An efficient integer programming approximation method that yields similar ...
Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses ...