When evaluating each of the cell-type deconvolution methods on the SRT datasets described above, since the true cell-type proportions are unknown, the relative performance of each method was assessed through visual examination of the deconvolution results and general knowledge of the approximate location...
Many spatially resolved transcriptomic technologies do not have single-cell resolution but measure the average gene expression for each spot from a mixture of cells of potentially heterogeneous cell types. Here, we introduce a deconvolution method, condi
细胞基质(ECM)、趋化因子和细胞因子信号通路则在所有脑区的APOE4小胶质细胞中均呈阳性富集(图3G-J)。在细胞类型反卷积分析(cell-type deconvolution)后,发现APOE4型AD星形胶质细胞依旧显示出相同的基质体相关模块,即趋化性、炎症和脂质合成(图3K-...
Here, we propose a cell type deconvolution evaluating toolkit named 'Deconer' to perform comprehensive and systematic evaluation of different algorithms. Deconer consists of 6 main functional components as described below: Pseudo bulk data generation (from large-scale bulk data and single-cell data)...
Cell composition deconvolution (CCD) is a type of bioinformatic task to estimate the cell fractions from bulk gene expression profiles, such as RNA-seq. Many CCD models were developed to perform linear regression analysis using reference gene expression signatures of distinct cell types. Reference gen...
EpiSCORE is an R-package for constructing a tissue-specific DNA methylation reference matrix that can be subsequently used in conjunction with a reference-based cell-type deconvolution algorithm to (i) obtain cell-type fraction estimates in a corresponding bulk-tissue sample for which a genome-wide...
13. Liu, L. et al. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity.bioRxiv316208 (2018). doi:10.1101/316208 14. Cusanovich, D. A. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution.Nature555, 538–542 (2018). ...
Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat Commun. 2020;11:5650. Article CAS PubMed PubMed Central Google Scholar Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics. 2010;11:367. Article PubMed PubMed ...
For spatial transcriptome data, deconvolution is required to determine the cell type composition of each spot based on the generated expression matrix. Therefore, the general data processing pipeline of spatial barcoding-based transcriptomics can be split into (1) upstream preprocessing to generate the ...
Fractions of different cell types were estimated with CIBERSORT (Newman et al., 2015), a cell type deconvolution program that derives cell type-specific abundances from bulk RNA-seq data. Here bulk RNA-seq data were downloaded from the whole TCGA LUAD cohort. Among the 594 samples with FPKM...