Seurat 常用命令列表---Seurat Command List Seurat_Satija关注IP属地: 安徽 0.3762021.03.13 09:21:30字数1,036阅读2,265 Compiled: 2021-02-08Seurat Standard WorflowThe standard Seurat workflow takes raw single-cell expression data and aims to find clusters within the data. For full details, please ...
Seurat 常用命令列表---Seurat Command List - 简书 (jianshu.com) Seurat4.0系列教程6:常用命令 - 简书 (jianshu.com) scRNA的3大R包对比 - 简书 (jianshu.com) 单细胞转录组分析中的各种数据结构 - 简书 (jianshu.com) AddMetaData示例 (单细胞测序-SingleCell)Seurat流程文献复现 - 简书 (jianshu.com)...
immune.anchors <- FindIntegrationAnchors(object.list = ifnb.list, anchor.features = features) 其次,是运用CCA方法整合多样本数据集的IntegrateData( ),输入锚点即可返回整合好的数据集: # this command creates an 'integrated' data assay immune.combined <- IntegrateData(anchorset = immune.anchors) immune....
list = ifnb.list, anchor.features = features, reduction = "rpca") 代码语言:javascript 代码运行次数:0 复制Cloud Studio 代码运行 # this command creates an 'integrated' data assay immune.combined <- IntegrateData(anchorset = immune.anchors) 现在,我们可以对所有细胞进行单次整合分析! 代码语言:...
IsGlobal(object = x[[o]])) }, x = objs.assay ) # 删除这些对象 for (o in objs.assay) { x[[o]] <- NULL } } # If adding a command, ensure it gets put at the end of the command list # 如果添加命令了,注意添加到最后 if (inherits(x = value, what = 'SeuratCommand')) {...
immune.anchors<-FindIntegrationAnchors(object.list=ifnb.list,anchor.features=features)#thiscommand creates an'integrated'data assay immune.combined<-IntegrateData(anchorset=immune.anchors) 执行整合分析 现在,我们可以对所有细胞进行单次整合分析! 代码语言:javascript ...
# Normalize ADT data,DefaultAssay(cbmc)<-"ADT"cbmc<-NormalizeData(cbmc,normalization.method="CLR",margin=2)DefaultAssay(cbmc)<-"RNA"# Note that the following command is an alternative but returns the same resultcbmc<-NormalizeData(cbmc,normalization.method="CLR",margin=2,assay="ADT")# Now, ...
..@ assays :List of 1 首先看对象里面的每个sample的属性(meta.data元素) > dim(brain@meta.data) [1] 2696 5 > head(brain@meta.data) orig.ident nCount_Spatial nFeature_Spatial slice AAACAAGTATCTCCCA-1 anterior1 13069 4242 1 AAACACCAATAACTGC-1 anterior1 37448 7860 1 ...
{"colorScheme":"Tango Dark","commandline":"cmd.exe /K C:\Users\<user_name>\anaconda3\Scripts\activate.bat, "cursorShape": "filledBox", "experimental.retroTerminalEffect": false, "guid": "{XXXX-XXXX}", "hidden": false, "icon": "C:\Users\<user_name>\anaconda3\Menu\anaconda-navigat...
在Seurat的官网可以看到SCTransform关于的描述,是:Note that this single command replaces NormalizeData(), ScaleData(), and FindVariableFeatures() 但是因为我接触单细胞有点早,是2017附近,那个时候经历了Seurat的v2变成v3的大更新,跟现在的小伙伴们经历了v4变成v5是一样的困扰,所以其实我从来就没有在我的代码...