从上面图形可以明显看出,四个批次数据存在差异,接下来利用Seurat(V5)提供的分析方法进行整合。 Seurat v5使用IntegrateLayers功能实现了简化的整合分析。该方法目前支持五种整合方法。每一种方法都在低维空间中执行整合,并返回降维结果(例如integrated.rpca): Anchor-based CCA integration (method=CCAIntegration) Anchor-...
首先我们下载安装相关的软件,读入数据,数据读取没有什么变化! #install packagesinstall.packages('Seurat')library(Seurat)#安装一些额外的包setRepositories(ind=1:3,addURLs=c('https://satijalab.r-universe.dev','https://bnprks.r-universe.dev/'))install.packages(c("BPCells","presto","glmGamPoi"))...
I am trying to integrate two single cell objects using the new V5 IntegrateLayers command. I have one dataset from mouse lungs and one from mouse muscle, and this information is stored in the $tissue metadata. I converted each assay to v5 using the as() command, wrote the assays to the...
> obj <- IntegrateLayers( object = obj, method = scVIIntegration, new.reduction = "integrated.scvi", conda_env = "/home/jovyan/my-conda-envs/scvi-env", verbose = FALSE ) Error in object[][features, ] : incorrect number of dimensions In addition: Warning message: In LayerData.Assay5...
...could anyone please help me...(T~T)...I can't live without a Seurat I use R4.3.2, Seurat v5, and I got the bug: Error in .local(x, na.rm, dims, ...) : object 'CRsparse_colSums' not found the same code and same data and same verson of ...
Hi, I want to map a query data to an integrated reference, but encountered a problem. The code and the error report are as following. Please help. Thank you. ### code to map a query data to an integrated reference ### li...