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 ...
The DISCERN algorithm for directed expression reconstruction We aim to realistically reconstruct gene expression in scRNA-seq data by using a related hq dataset. Ideally, this expression reconstruction algorithm should meet several requirements [7]. First, it needs to bepreciseand model gene expression...
(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 ...
some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. 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 ofArabidopsis thalian...
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-...
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...
algorithm can be performed iteratively in classifying the cell types.b, Heatmap demonstrating the prediction accuracy for the first-level cell types. The rows represent the cell types reported in the publications, while the columns represent the scAnnot-predicted cell types. The color intensity ...