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Seurat对象 查看seurat对象的结构: str(object) seurat对象的元信息: object@meta.data 指定使用的idents: Idents(object) <- "seurat_clusters" 指定使用的assay: DefaultAs ...

数据读取123library(magrittr)library(tidyverse)data <- readr::read_tsv("test.tsv") %>% as.data.frame() # %>%为管道操作符 合并数据123456789# 左连接 ( ...

Load 10X visium data123456789101112library(Seurat)library(ggplot2)library(patchwork)# dataDir contains spatial dir and filtered_feature_bc_matrix.h5# ...

Space Ranger countSpatial GEX12345678910# Pipeline for fresh frozen (FF) tissue section# Fastq name must be: sample_S1_L00[lane_number]_[I1/R1/R2]_001 ...

Load expression data123456789library(Seurat)library(ggplot2)# Read count data (row is gene, column is cell)data <- read.table(file = "sample.c ...

测序数据生成表达矩阵Cell Ranger count1234567# Fastq name must be: sample_S1_L00[lane_number]_[I1/R1/R2]_001.fastq.gz# I1 is optionalcellranger count \--sample=s ...

测序数据生成表达矩阵质控Fastp1234567fastp -i sample.raw.r1.fq.gz \-I sample.raw.r2.fq.gz \-o sample.clean.r1.fq.gz \-O sample.clean.r2.fq.gz \-j sample.QC.json \- ...

以下均以人Hg38(GRCh38)版本为例 Ensembl https://asia.ensembl.org/Homo_sapiens/Info/Index Fasta: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz (https://ftp.ense ...