WebTo enable pseudobulk differential expression (DE) analysis, we need to transform our single-cell level dataset into one sample-level dataset per cell type (cluster) that we want to study using DE analysis. Extracting necessary metrics for aggregation by … WebAug 24, 2024 · As breast cancer is a heterogenous disease, the bulk gene expression may not be the ideal resource for cancer prognosis. In this study, we propose a novel method to improve breast cancer prognosis using scRNA-seq data. The proposed method has been applied to the EMT scRNA-seq dataset for identifying breast cancer …
Single-cell vs. bulk sequencing: which one to use when?
Although a reference profile from snRNA-seq can help to decompose bulk-level gene expression, it may not be available for the same dataset. The majority of bulk RNA-seq datasets do not have corresponding snRNA-seq data in the same set of individuals. However, marker gene information from prior … See more A graphical overview of Bisque is presented in Fig. 1. Our reference-based decomposition model requires bulk RNA-seq counts data and a reference dataset with read counts … See more We also benchmarked these decomposition methods using expression data collected from the dorsolateral prefrontal cortex … See more We applied our method to 106 bulk RNA-seq subcutaneous adipose tissue samples collected from both lean and obese individuals, where 6 samples have both bulk RNA-seq and … See more Given the large amounts of transcriptomic data that are becoming available, we also benchmarked these decomposition methods in terms of … See more WebAug 25, 2024 · Characterizing PDAC by mRNA profiling remains particularly challenging. Previously identified bulk expression subtypes were influenced by contaminating … a taille humaine meaning
Determining cell type abundance and expression from bulk
WebMay 23, 2024 · This method utilizes marker genes alone to decompose bulk expression when a reference profile is not available. Single-cell data is not explicitly required but can be used to identify these marker genes. This method captures relative abundances of a cell type across individuals. WebTo perform sample-level differential expression analysis, we need to generate sample-level metadata. To do this, we will reorder samples in the single-cell metadata to match the … WebMay 10, 2024 · Simulation of bulk expression profiles indicates that mesenchymal signatures are dominated by CAFs Before analysing bulk expression profiles, we sought to understand the expected expression... a taineira