Cell clusters were determined by shared nearest-neighbor using the Louvain algorithm. Unbiased clustering was performed separately for each sample and for the combined samples to facilitate comparisons of subpopulations in HPV16+ and HPV16− rafts. Cluster gene lists (Supplementary Data 2) were ...
To address these challenges, we developed Tempo, a Bayesian algorithm for single-cell phase inference from scRNA-seq data. Through a combination of both simulated and real data analyses, we demonstrate that Tempo yields state-of-the-art point estimates. Moreover, Tempo empowers better phase estim...
In essence, the algorithm predicts a gene will have a given function based on the proportion of its connectivity to genes that already have that function (i.e. the sum of the gene’s edge weights within the function divided by the gene’s node degree). This can then be assessed for ...
single-pass algorithms were introduced to enable a stream-oriented hardware design. However, most single-pass CCA algorithms in the literature inhibit maximum
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. For more information about the gsva algorithm, see the GSVA package (PMID: 23323831) # Since the GSVA algorithm is time-consuming on large ...
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...
We also used the spherical K-means algorithm [15] on TF-IDF scores of genes selected using Top, respectively Var. Hierarchical clustering (TF-IDF_Top_HC_E, TF-IDF_Top_HC_P, TF-IDF_Top_HC_C, TF-IDF_Var_HC_E, TF-IDF_Var_HC_P, TF-IDF_Var_HC_C). Finally, we performed hierarch...
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” ...
The Faiss index code in our work was “IVF1024 HNSW32, SQ8”, a graph-based index with a Hierarchical Navigable Small World (HNSW) algorithm38. In our approach, we pre-computed and indexed the dense vector representations of all reactants on the training and validation data with the ...
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 ...