Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology Article Open access 25 April 2022 Pan-cancer classifica
Here, we used computational deconvolution to identify cell types in COPD and IPF lungs whose abundances and cell type-specific gene expression are associated with disease diagnosis and severity.#We analyzed lung tissue RNA-seq data from 1026 subjects (COPD,n=465; IPF,n=213; control,n=348) ...
To study the genetic regulation of gene expression throughout T cell activation, we performed cis-eQTL mapping. For each time point, we reconstructed average transcriptional profiles per cell type and individual (i.e., pseudobulk transcriptomes) corresponding to TN and TM CD4+ T cells (Methods)...
Burdick JT, Murray JI. Deconvolution of gene expression from cell populations across the C. elegans lineage. BMC Bioinformatics. 2013; 14 :204. doi: 10.1186/1471-2105-14-204. [ Cross Ref ]Burdick JT, Murray JI. Deconvolution of gene expression from cell populations across the C. elegans ...
Warning: single-cell reference and bulk samples should contain the same cell types # basic examplefromTAPEimportDeconvolutionSignatureMatrix,CellFractionPrediction=\Deconvolution(sc_ref,bulkdata,sep='\t',scaler='mms',datatype='counts',genelenfile='./GeneLength.txt',mode='overall',adaptive=True,vari...
Section 7: Well-Characterized Deconvolution Datasets Citation Links: Deconer manual Deconer vignettes Deconer datasets Section 1: Introduction Cell type proportion is related to phenotypes or diseases (Wang, et al., Wei, et al.). Therefore, quantifying cell or tissue proportions is important for ...
STdGCN is designed for cell-type deconvolution in ST data by using scRNA-seq data as a reference (Fig.1). The underlying hypothesis is that both ST data and scRNA-seq data share common cell types, and their cell type gene transcript signatures exhibit similarities. In short, the normalized...
Schematic diagram for SCADIE: (a) SCADIE requires either (1) bulk gene expression matrices and cell type proportions or (2) bulk gene expression matrices and shared signature matrix as input; the cell type proportions can be obtained by any deconvolution method. (b) The initial fullWmatrices...
Cell Type Diversity Cell Types Flow cytometry Gene expression profiling Immune cell isolation Transcriptomics Introduction Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene expression at single-cell resolution, which improves the detection of known and novel cell types and ...
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data Charles E. Breeze, Dirk S. Paul, Jenny van Dongen, Lee M. Butcher, John C. Ambrose, James E. Barrett, and others Cell Reports, Vol. 17, Issue 8 The International Human Epigenome Consortium Data Portal ...