Converge SCCAF_optimize min_acc! m1: 0.134328 m2: 0.004653 Accuracy: 0.954424 看一下最后的结果,由原本的12类变成了10类 sc.pl.tsne(ad,color=['L1_result','cell',],frameon=False,title=['SCCAF','Human Annotation']) 最后我们总结一下基本流程: 走标准流程得到聚类信息 文章 将聚类信息设置为初始化...
Prostate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we perform single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organo...
Single-cell RNA sequencing Libraries for scRNA-seq were generated using the Chromium Single Cell 3′ library and Gel Bead & Multiplex Kit from 10x Genomics. 10×Genomics Chromium barcoding system was used to construct a 10× barcoded cDNA library following the manufacturer’s instructions. All lib...
更重要的是,他们broadly asked whatgenesmight be associated with subclonal dissemination (EH) in M2, by performing a regression of EHagainst single-cell gene expression with adjustment for confounders.他们鉴定到973 genes positively associated with dissemination and 1,037 negatively associated genes。从中...
Table S4. List of Gene Signatures; Sources for T Cell Signatures Are Stated in STAR Methods, and M1 and M2 Signatures Are Listed with Sources in the Second and Third Sheets, Related to Figures 4, 5, and 6 Table S5. Full Hallmark GSEA Enrichment Results for Gene Variance in T Cells (...
The DifferentGeneTest function was used for differential expression analysis, and the top 2000 significant genes were selected to define cell progression. The DDRTree method was used to reduce the dimensions. The pseudotime trajectory was visualized with the plot_cell_trajectory function in the Monocle...
分析各髓系细胞亚群与肠粘膜间距发现,健康对照组驻留巨噬细胞与粘膜相距最近,肥大细胞和DCs倾向位于更深层次粘膜层,而IBD患者M1巨噬细胞和中性粒细胞可见于粘膜表面即溃疡处。 Fig.2 | Analysis of myeloid cell subsets in healthy and inflamed colonic mucosa. ...
In addition, HASCAD model is an ensemble of three subnetworks, namely M1, M2, and M3 (Fig.2), where the three sets of output values were averaged to give the predicted cell fractions. It was noted that the performance of each individual subnetwork was more varied than the ensemble model...
the TME, we performed cell-cell communications using ligand-receptor pairing analysis, and found that the epithelial cells (containing subtype 1 and 2 epithelial cells) more actively communicated with other cell types including Tregs, monocyte-like cells and M1/M2 macrophages in Tm than Tn (Fig....
Single myeloid phagocytic cells with low Msc2IR scores demonstrated upregulation of proinflammatory cytokines/chemokines and downregulation of antigen presentation genes, were unrelated to M1 versus M2 polarization, and were enriched in pretreatment blood samples from patients with PD-L1 blockade-resistant ...