而目前在R中分析single cell RNA-seq 的包有 SingleCellExperiment , scater,Seurat这三个 其中SingleCellExperiment我在之前的推送中讲解过 而scater的分析流程如下:
RNA sequencingTUMOR microenvironmentDRUG targetPHENOTYPESExamining tumor-associated macrophages in the immune microenvironment of non-small cell lung cancer (NSCLC) is essential for gaining an understanding of the genesis and development of NSCLC as well as for identifying key clinical therapeutic targets. ...
在本周一的文章(复现原文(一):Single-cell RNA sequencing of human kidney(step by step))中,我们完成了scRNA-seq数据的质控(Hemberg-lab单细胞转录组数据分析(三)- 原始数据质控)、批次校正、找Marker基因(单细胞分群后,怎么找到Marker基因定义每一类群?)、UMAP可视化和tSNE可视化(Hemberg-lab单细胞转录组数据分...
aes(x=PC1,y=cell_type2,colour=cell_type2))+geom_quasirandom(groupOnX=FALSE)+scale_color_tableau()+theme_classic()+xlab("First principal component")+ylab("Timepoint")+ggtitle("Cells ordered by first principal component")
在本周一的文章(复现原文(一):Single-cell RNA sequencing of human kidney(step by step))中,我们完成了scRNA-seq数据的质控(Hemberg-lab单细胞转录组数据分析(三)- 原始数据质控)、批次校正、找Marker基因(单细胞分群后,怎么找到Marker基因定义每一类群?)、UMAP可视化和tSNE可视化(Hemberg-lab单细胞转录组数据分...
确定一下 cell 名的组成,构建好 metadata(行名) 和 count(列名) 矩阵能够对应 过滤掉外源 RNA (ERCC) 合并成为 seurat 对象 计算线粒体(MT),核糖体的 RNA(^RP[SL]) 比例并筛选数据 我们先处理第一个表达矩阵 # 这个是治疗前的第一个表达矩阵
The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so
Single Cell RNAseq Stem Cells Systems biology Before you begin This protocol describes a method for analyzing single-cell RNA sequencing (scRNA-seq) datasets using an R package called SingCellaR. In addition to standard functions (e.g., reading gene expression matrices, data filtering, doublet ...
With single-cell RNA-Seq technology improving, we can only expect increased cell throughput and larger datasets. While DendroSplit is able to generate clusters without expensive hyperparameter tuning, its optimal split and merge thresholds do depend on the size of the dataset since larger datasets ...
For this dataset, cells from pancreatic islets were dissociated and sorted by FACS into 384-well plates. Single-cell RNA-seq libraries were generated using the Smart-seq2 protocol and sequenced on an Illumina HiSeq 2000. We used all 2,045 cells annotated with one of seven cell types (185 ...