SingleR是一个用于对单细胞RNA-seq测序(scRNA-seq)数据进行细胞类型自动注释的R包(Aran et al.2019),是基于表达值的correlation的。它通过给定的具有已知类型标签的细胞样本作为参考数据集,对测试数据集中与参考集相似的细胞进行标记注释。具体来说,对于每个测试细胞: 首先,我们计算每个细胞的表达谱与参考样品的表达谱...
6 SAMap scores for all cell type groups. a, b, Heatmaps of SAMap mapping scores for all groups of non-neuronal and neuronal cell types between mouse and lamprey, including all genes (a) and TF genes only (b). Extended Data Fig. 7 Correlations between cell type groups. a, b, Heat...
In conducting supervised contrastive learning, we approximated the cell type representation by using the arithmetic mean of gene profile vectors from all cells annotated with a specific cell type. We utilized the PBMC dataset to investigate the cell type hierarchy for this method in both the raw an...
we looked at how the TF mRNA expression levels, as measured by RNA sequencing, correlated with the number of peaks. We found some, but insignificant, correlation between TF expression
3. Run correlation and random-forest feseR to narrow down the genelist.(使用机器学习算法缩小预测变量范围) 4. Generate RFmodels based on feseR-restricted genesets(产生随机森林模型) 5. Check accuracy in fetal vs adult cells that were not in the training set(检验模型的性能,并不是在训练集上,...
'percent_ecoli_reads','percent_aligned_reads_total','complexity_cg','genes_detected_cpm_criterion','genes_detected_fpkm_criterion','tdt_cpm','gfp_cpm','class','subclass','cluster','confusion_score','cluster_correlation','core_intermediate_call','id','cell_type','dbscan_filter'var:'vst....
The statistical analysis in this study was conducted using R (version 4.2.2), GraphPad Prism (version 9), and Python (version 3.7). We utilized the Mann-Whitney U test to compare differences between two groups, and the Spearman method for correlation analysis. For survival analysis, we employ...
the case with no prior information of cell type number of the tissue, we adopt goodness of fit in addition to correlation with true or RB proportions as metrics, as calculating goodness of fit does not require known true proportions (details demonstrated the “Method and material” section). ...
a Hierarchical clustering of the correlation between each transformed subpopulation and a database of cell type-specific expression profiles with high variability across the data set. We find three cell type clusters referred to as Neural/ESC, Immune, and Mesenchymal/MSC which divide the tumor cell...
We also identified a significant correlation between the GC B cell and TFH signatures (R = 0.84, p < 0.0001), which suggested the co-existence of these two cell types in tumors (Figure 1H). GC B cell and TFH signatures were also correlated with Th1 and CD8 effector T cell signatures (...