DimPlot(pbmc, reduction = "umap",group.by = 'celltype' ,pt.size = 0.5,label = FALSE) ggsave(filename = 'FIG/Annotation_umap.png',width = 10,height = 8) #预测细胞类型2,使用method = "single"方法,聚在同一类的细胞可能会注释成不同种细胞类型 Anno2 <- SingleR(test = data_for_SingleR...
wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_fragments.tsv.gz wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1...
we will be analyzing the a dataset of Peripheral Blood Mononuclear Cells (PBMC) freely available from 10X Genomics. There are 2,700 single cells that were sequenced on the Illumina NextSeq 500. The raw data can be found here.
图4. 10x Genomics single cell 3’ gel bead Poly(dT)-primer 用于识别细胞表面蛋白的特征条带编码(bardcoding)的两个额外引物 cell barcode and UMI GEMs油滴 image.png 图5. 10x Genomics Chromium Next GEM Chip G 一个油滴 (GEM)=一个单细胞+一个凝胶微珠=一个scRNA-Seq,可以说这就是10X的基本技术...
在学习/测试新方法时,起步常需要一些测试数据。如果手边没有自测的数据,或者不便使用时,可以考虑使用一些开源的测试数据。比如单细胞测序中比较经典的PBMC数据,在 10x Genomics 公司在其官网上可以简单注册后直接获取: https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/pbmc3k ...
对于SingleCellExperiment这种数据类型,它会首先在数据中寻找size factor是否存在,如果找不到,也是会使用librarySizeFactors 也就是说,如果我们不提前计算,就会自动帮我们用最简单的librarySizeFactors计算,并添加到我们的数据中。正是因为我们只需要最简单的方法,所以才可以不提供。如果要使用去卷积方法,还是要自己先计算...
是文章: Single cell transcriptomic landscape of diabetic foot ulcers.Nat Commun2022 ,它的第一层次降维聚类分群要复杂一点,一步到位了: 本质上也是读取文件即可,代码是: library(data.table) dir='GSE165816_RAW/'samples=list.files( dir ) sampleslibrary(data.table) ...
wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5 wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv
wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5 wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv
wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5 wget https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv