针对你遇到的错误 error in 'object[[reduction]]': ! ‘tsne’ not found in this seurat object,这个问题通常意味着你尝试访问的Seurat对象中没有包含tsne这个降维结果。以下是根据你的提示,逐步分析和解决问题的建议: 检查Seurat对象中是否包含'tsne': 你可以使用以下R代码来检查Seurat对象中是否包含tsne降维结...
1.报错 在安装Seurat会出现如下核心报错: configure: error: geos-config not found or not executable. 2.原因 尝试手动下载解压安装rgeos、从Github上安装Seurat、修改镜像,都不解决问题,因为着根本不是下载的错误。 因为Seurat依赖SeuratObject,SeuratObject又依赖rgeos,集群没有配置没有rgeos的环境,所以报错。 3.解...
但是这个下载的版本应该是3.9.1的,跟rgeos中所需的版本3.11不一样,但是可以用就是。 2. 安装rgeos_0.5-9.tar.gz,SeuratObject_4.1.2.tar.gz和Seurat_4.2.0.tar.gz install.packages("rgeos_0.5-9.tar.gz",repos=NULL)install.packages("SeuratObject_4.1.2.tar.gz",repos=NULL)install.packages("Seurat_...
Hi there, I've recently upgraded to Seurat 5 and I'm now receiving the above error when trying to runCreateSeuratObject()on a script that perviously ran without error. This script downloads publicly available data from a repository and runs the basic Seurat process. It worked previously when...
After upgrading to Seurat/SeuratObject v5.0.1 users who also have Azimuth and/or Signac installed may encounter the following error: object 'CRsparse_colSums' not found when trying to run colSums or rowSums on any dgCMatrix. This in turn breaks quite a bit of Seurat's basic functionality. ...
The 10x gene expression matrices from all samples were combined as one Seurat object for analysis. We filtered cells with feature counts over 50000, UMIs less than 600, or mitochondrial UMIs exceeding 15%. For each remaining cell, gene expression was normalized by total number of counts, ...
To address this issue, we performed a meta-analysis of publicly available expression array data and found that across a range of pro-inflammatory activation stimuli, TSPO expression is consistently and substantially increased in mouse, but not human macrophages and microglia in vitro. We then perform...
Adult microglia rely on self-renewal through division to repopulate and sustain their numbers. However, with aging, microglia display morphological and transcriptional changes that reflect a heightened state of neuroinflammation. This state threatens agi
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'head': Cannot find 'monocle3_pseudotime' in this Seurat object no-responsebot commentedNov 23, 2020 Can you show me the commands you ran for calculating pseudotime with Monocle ...
I try to create a Seurat Object and when I use Read10X : a<-CreateSeuratObject(counts = Read10X("D:/ATAC-seq/SCRNA_GBM//GSM5319529_SF8963",gene.column=1),min.cells = 3, min.features = 200) there is an error message as follows: Error: rea...