此教程展示了使用 scVelo 分析存储在 Seurat 对象中的 RNA 速率值。如果您在工作中使用 scVelo,请引用下文: Generalizing RNA velocity to transient cell states through dynamical modeling Volker Bergen, Marius Lange, Stefan Peidli, F. Alexander Wolf & Fabian J. Theis doi: https://doi.org/10.1101/8209...
But, before we do that, we will export all of the necessary meta-data from our Seurat object that is needed for our RNA Velocity object. This includes: Filtered Cell Ids UMAP or TSNE coordinates Clusters (Optional) Cluster Colors (Optional) ...
1. 在 Seurat 中导出必要的数据 (1) 导出 RNA 计数矩阵 library(Seurat) library(Matrix) # 导出 RNA 计数矩阵 counts <- GetAssayData(seurat_object, slot = "counts", assay = "RNA") writeMM(counts, file = "counts.mtx") # 导出基因名 write.csv(rownames(counts), file = "genes.csv", row...
在上文中，我们定义了RNAvelocity为\boldsymbol{v}(t)=\frac{\mathrm{d} s}{\mathrm{~d} t}=u...
library(Seurat)library(SeuratObject)library(ggplot2)# remotes::install_github('satijalab/seurat-wrappers')library(SeuratWrappers)#RunVelocity #library(devtools)#install_github("velocyto-team/velocyto.R")library(velocyto.R)library(stringr) 我们主要是使用了 SeuratWrappers 里面的 as.Seurat 函数把RNA速率...
A guide to using a Seurat object in conjunction with RNA Velocity kallistoseuratbustoolsanndatarna-velocitykb-pythonintegrating-loomvelocytoscvelokallisto-bustools UpdatedDec 25, 2021 Dragonmasterx87/Interactive-3D-Plotting-in-Seurat-3.0.0 Star121 ...
这个告诉我们当前对象主体是13425(基因数)*39233(细胞数)的矩阵,有一个叫RNA的assay,在这个assay中,我们选择了3000个基因作为variable features(一般用来计算PCA),计算了三种降维:PCA, UMAP, t-SNE。 Assay The Assay object is the basic unit of Seurat; each Assay stores raw, normalized, and scaled data...
按照细胞ID提取：subset(x = object, cells = cells)按照idents提取：subset(x = object, idents = c(1, 2))按照meta.data中设置过的stim信息提取：subset(x = object, stim == "Ctrl")按照某一个resolution下的分群提取：subset(x = object, RNA_snn_res.2 == 2)当然还可以根据某个基因...
immune.anchors <- FindIntegrationAnchors(object.list = ifnb.list, anchor.features = features) immune.combined <- IntegrateData(anchorset = immune.anchors) 1. 2. 3. 整合分析 我们对修正后的数据进行下游分析,原始数据仍然存在于“RNA”assay中 ...
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