Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the...
While BulkTrajBlend can efficiently extract the state space of cells from Bulk RNA-seq and interpolate the original scRNA-seq data, this interpolation relies on the selection of the reference scRNA-seq versus the reference Bulk RNA-seq data. We suggest that users can adopt an additional comprehen...
yet the interplay between copy number alterations (CNAs), replication timing (RT) and cell cycle dynamics remain understudied in aneuploid tumors. We developed a probabilistic method, PERT, for simultaneous inference of cell-specific replication and copy number states from single-cell whole genome seq...
we identified 48 sex-biased DSEs in 32 genes across all cell types (false discovery rate (FDR) < 0.05; Fig.2dand Supplementary Table2). An example of shared sex-biased splicing involved filamin A (FLNA), an auto-antigen targeted by T and B cells in more than 50% of ...
(Top) The same network as in panel b, trained with dropout on hidden nodes. Dropout nodes are randomly selected at each training iteration. (Bottom) Learning with dropout results in robust and highly correlated weights (inset) for the two redundant nodes.dNode weights of weakly and strongly ...
(Fig.1). The batch correction algorithms tested are either available in the R or Python language environment. For Seurat 2, Harmony, MNN Correct, fastMNN, and limma, the data preprocessing steps of normalization, scaling, and highly variable gene (HVG) selection were performed using the Seurat...
Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing effo
Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data ArticleOpen access31 July 2024 18 July 2024 Introduction DNA replication and cell cycle regulation are frequently disrupted as part of a cancer’s progression toward uncontrolled proliferation1,2,3. ...
The IRB will require details about the questionnaire, participant selection, data collection and analysis processes. As we prepare to formally implement practical Precision Medicine training in our medical school curriculum and expand it to our other campuses, we have identified some potential ...
(Top) The same network as in panel b, trained with dropout on hidden nodes. Dropout nodes are randomly selected at each training iteration. (Bottom) Learning with dropout results in robust and highly correlated weights (inset) for the two redundant nodes.dNode weights of weakly and strongly ...