针对你遇到的问题“validating h5seurat file error: invalid h5seurat file: cannot find attribute”,以下是一些详细的解决步骤和建议: 确认h5seurat文件的完整性: 使用HDF5的官方工具(如h5dump或h5stat)或其他第三方工具来检查h5seurat文件的完整性。这些工具可以帮助你确定文件是否已损坏或缺失某些属性。 示例命令...
最后使用r读入这三个文件,然后创建seurat对象 注:因为是多个样本,所以需要我们在python中循环读取h5文件成一个list,然后concatenate成一个大的adata对象,最后导出 代码实战 python中代码循环读取h5,整理成一个adata对象 代码语言:javascript 代码运行次数:0 运行 AI代码解释 importscanpyasscimport os# Define the di...
ids <- list.files(path = "Newdata", full.names = TRUE, pattern = "\\.h5$") # 函数:创建和处理Seurat对象 create_and_process_seurat <- function(file_path) { data1 <- Read10X_h5(file_path, use.names = TRUE) biofscicol <- gsub("\\.h5$", "", basename(file_path)) biofsci ...
第二步,在R中读取导出的数据,并创建seurat对象 代码语言:javascript 代码运行次数:0 运行 AI代码解释 cellinfo=read.csv("/home/data/t040413/heart_muscle/item1_NF_DCM_HCM/fibroblast/cellinfo.csv",row.names="X")head(cellinfo)geneinfo=read.csv("/home/data/t040413/heart_muscle/item1_NF_DCM_...
Validating h5Seurat file Error: Ambiguous assays 解决办法: 在运行中添加参数 assays = "RNA", verbose =TRUE # 自己安装 mojaveazure/seurat-disk 这个GitHub包: #remotes::install_github("mojaveazure/seurat-disk") library(SeuratDisk) library(patchwork) ...
(filename = paste0(pro,'_umap_seurat_res.0.8.pdf') ) DimPlot(sce, reduction = "umap",split.by = 'orig.ident') ggsave(filename = paste0(pro,'_umap_seurat_res.0.8_split.pdf') ) library(gplots) tab.1=table(sce@meta.data$integrated_snn_res.0.8,sce@meta.data$integrated_snn_res....
h5ad是python的Scanpy读取文件格式,对其进行格式转换,并得到.h5seurat格式的文件 > Convert("./data/integrated/morse_n_adams_n_bal_scvi_patient.id_227086_400_revision.h5ad", "h5seurat", + overwrite = FALSE,assay = "RNA") Warning: Unknown file type: h5ad Creating h5Seurat file for version ...
Hi Emily,Have you solved your problem? Have you been able to convert h5 files into Seurat objects? I have the same problem as you,I hope you could give me some advice. Thanks, Zerun Song Sorry, something went wrong. Copy link
library(Seurat) library(dplyr) # 读取Newdata文件夹中的所有h5文件 ids <- list.files(path = "Newdata", full.names = TRUE, pattern = "\\.h5$") # 函数:创建和处理Seurat对象 create_and_process_seurat <- function(file_path) { data1 <- Read10X_h5(file_path, use.names = TRUE) ...