单细胞DEGs、markers、celltypes | 专辑完结篇 单细胞水平样本间的差异分析 主要参考: 生物学重复的不同条件下的scrna-seq数据的差异基因表达分析 (https://www.10xgenomics.com/resources/analysis-guides/differential-gene-expression-analysis-in-scrna-seq-data-between-conditions-with-biological-replicates) 需要注...
we generate in silico single-cell gene expression data for each cell type using BoolODE using the simulated GRNs and add 80% zeros in the simulation data. Then, we apply five multi-task learning algorithms and three single-task learning algorithms for GRN inference to ...
Hu C, Li T, Xu Y, et al. CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data [published online ahead of print, 2022 Oct 27].Nucleic Acids Res. 2022;gkac947. doi:10.1093/nar/gkac947 最后祝大家早日不卷!~...
Yet, these markers will be redundant if the latent dimension of the space spanned by the gene expression profiles of each cell type is lower than the number of cell labels we aim to distinguish. Assuming this is true, then a number of markers smaller than k is needed to maintain the ...
library(genesorteR)data(kidneyTabulaMuris)#three cell types from kidney (Tabula Muris data)#get specificity scores for each cell typesg=sortGenes(kidneyTabulaMuris$exp,kidneyTabulaMuris$cellType)head(sg$specScore)#specificity scores for each gene in each cluster#define a small set of markersmm=ge...
1.1 What Is a CellType? 虽然每个细胞都是独一无二的,但多年来生物学家的经验表明,细胞可以根据可量化的共同特征来分组。这种分类使对复杂组织的系统和可重复的分析成为可能,类似于物种的概念,这大大简化了生物体的多样性,使之成为一种可解释的分类法,同时又不否认任何单一成员[18]的个性。用于定义细胞类型的...
The first chapter of this thesis explored the dominant gene expression pattern in the adult human brain. We discovered that the largest source of variation can be explained by cell type marker expression. Across brain regions, expression of neuron cell type markers are anti-correlated with the exp...
Thus, analysis of gene expression patterns provides an informative way of studying cellular diversity [1, 2]. In these studies, it has been commonly observed that some genes are specifically expressed in certain cell-types. These genes serve as cell-type markers and might define cell-type-...
官方地址(教程):Running cellranger count -Software -Single Cell Gene Expression -Official 10x Genomics Support 1、定量前准备: 预先下载好参考基因组文件(并解压) 确定好下载的cellranger软件能用 2、编写一个文件,里面存放fastqc 文件的前几个字符 (就是官方给定的[sample name] ) 3、编写脚本文件:(举例cel...
3). Cells in the early activation group expressed fourfold fewer genes compared to other cells at their respective activation time points and showed lower expression of T cell activation markers19 (Supplementary Fig. 3). Furthermore, they showed a unique profile characterized by high expression of...