Seurat v5使用IntegrateLayers功能实现了简化的整合分析。目前支持五种方法。这些方法中的每一种都在低维空间中执行集成,并返回降维(即integrated.xxx),该降维旨在跨批次共同嵌入共享细胞类型。 Anchor-based CCA integration (method=CCAIntegration) Anchor-based RPCA integration (method=RPCAIntegration) Harmony (method...
library(harmony) library(Seurat) #ref 数据集 sce8w <- readRDS("F:/nafld_singlecell/subcell_20221031/liversc_clean.rds") #新数据集 scRNA <- readRDS("F:/nafld_singlecell/subcell_20221031/liversc_geo_mo.rds") DimPlot(sce8w, group.by = "celltype") DimPlot(scRNA, group.by = "seurat_...
3、Compare Result of Seurat v4 & v5 SCT-Normalization Based Integration 通过对CCA方法校正后的UMAP表示进行目视检查,Seurat v4和v5 版本都能比较好的校正不同技术平台引入的技术偏差,并且保留了细胞类型的可区分性。 DimPlot(seuObj.combined.sct,group.by = "seurat_annotations",label = T) & labs(title =...
seurat <- IntegrateLayers(object = seurat, method = HarmonyIntegration, assay = "SCT", orig.reduction = "pca", new.reduction = "harmony", verbose = TRUE ) Console output: ... Harmony 6/10 0% 10 20 30 40 50 60 70 80 90 100% [---|---|---|---|---|---|---|---|--...
Add HarmonyIntegration to perform Harmony integration. Add IntegrateLayers to integrate layers in an assay object. Add JointPCAIntegration to perform Seurat-Joint PCA Integration. Add LeverageScore to compute the leverage scores for a given object. Add LoadCurioSeeker to load Curio Seeker data. Add...
代码语言:javascript 复制 remove.packages('Seurat')pkgs=c('mixtools','lars','dtw','doSNOW','hdf5r')BiocManager::install(pkgs,ask=F,update=F)# 以后只需要修改这个版本号即可 packageurl<-"https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz"install.packages(packageurl,re...
within 3 assays Active assay: SCT (28570 features, 3000 variable features) 3 layers present: counts, data, scale.data 2 other assays present: ATAC, RNA 9 dimensional reductions calculated: pca, lsi, umap.atac, umap.rna, harmony.sct, umap.harmony.sct, harmony.atac, umap.harmony.atac, wnn...
[6] HGNChelper_0.8.1 SCpubr_2.0.1 clustree_0.5.0 ggraph_2.1.0 harmony_0.1.1 [11] Rcpp_1.0.11 BPCells_0.1.0 stringr_1.5.0 openxlsx_4.2.5.2 patchwork_1.1.3 [16] ggrepel_0.9.4 ggpubr_0.6.0 ggrastr_1.0.2 ggbeeswarm_0.7.2 ggplot2_3.4.4 ...
(message = "'assay' must be a v5 or SCT assay") } if (!is.null(scale.layer)) { features <- intersect(x = features, y = Features( x = object, assay = assay, layer = scale.layer )) } if (!length(x = features)) { abort(message = "None of the features provided are found...