We used the circle classification algorithm described previously to define circular DNA-enriched regions in single cells. For each single cell, we defined whether the circular DNA-enriched regions overlapped the ecDNA amplicon (MYNC, CDK4, MDM2) assembled from TR14 bulk sequencing data using the fu...
The CellRank algorithm aims to model the cell state dynamics of a system (Methods). CellRank detects the initial, terminal and intermediate cell states of the system and computes a global map of fate potentials, assigning each cell the probability of reaching each terminal state. Based on the i...
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 ...
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 ...
in which the algorithm was run using Euclidean and Pearson correlation distances on either the first 10 principal components of the log2(x+1) UMI counts (methods referred to asLog_PCA_HC_EandLog_PCA_HC_P, respectively), or on the 2-dimensional tSNE transformation of the data as in [7]...
(B) Boxplot showing the number of expressed genes in each oocyte subtype. Two-tailed t testP valueis indicated. The number between oocytes C2 and C3, and the number between oocytes C3 and C4 are not significantly different. (C) Immunofluorescence showing the higher expression levels of 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...
Middle panel: Inference algorithm with Gibbs iterations are depicted where cell-specific (j, j) and cluster-specific (k, k) parameters are iteratively inferred leading to cell assignments to clusters. Right panel: Output from Biscuit, which is the normalized and imputed count matrix. The custom-...
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...