pbmc.atac <- subset(pbmc.atac, seurat_annotations != "filtered") # Perform standard analysis of each modality independently RNA analysis pbmc.rna <- NormalizeData(pbmc.rna) pbmc.rna <- FindVariableFeatures(pbmc.rna) pbmc.rna <- ScaleData(pbmc.rna) pbmc.rna <- RunPCA(pbmc.rna) pbmc.rna...
Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC Biol. 2023 Feb 1;21(1):19. doi: 10.1186/s12915-023-01519-z. PMID: 36726129; PMCID: PMC9893630. 5、 Hata M, Hata M, Andriessen EM, Juneau R, Pilon F, Crespo-Garcia S, Diaz-Marin R, ...
pattern = "^MT-")$percent # 计算每个细胞的mt基因比例 atac <- subset(atac, ...
1.Stuart, T., Srivastava, A., Madad, S. et al. Single-cell chromatin state analysis with Signac. Nat Methods 18, 1333–1341 (2021). https://doi.org/10.1038/s41592-021-01282-5 2.Stuart T, Butler A, Hoffman P, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177...
/home/jdoe/runs/sample345/outs/raw_peak_bc_matrix-Directoryofanalysis files:/home/jdoe/runs/sample345/outs/analysis-Filtered peak barcode matrixinhdf5 format:/home/jdoe/runs/sample345/outs/filtered_peak_bc_matrix.h5-Filtered peak barcode matrixinmex format:/home/jdoe/runs/sample345/outs/...
pbmc.rna<-subset(pbmc.rna,seurat_annotations!="filtered")pbmc.atac<-subset(pbmc.atac,seurat_annotations!="filtered")# Perform standard analysisofeach modality independentlyRNAanalysis pbmc.rna<-NormalizeData(pbmc.rna)pbmc.rna<-FindVariableFeatures(pbmc.rna)pbmc.rna<-ScaleData(pbmc.rna)pbmc.rna<-...
近日,中山大学徐锦课题组在aBIOTECH杂志上发表了题为"Fundamental and practical approaches for single cell ATAC-seq analysis"(点击题目查看原文)的综述论文,为 scATAC-seq 数据处理与分析提供了实用指南,介绍了包括数据预处理、数据质量评估、染色质图谱分析和针对具体科学问题的下游分析方法。
主成分分析(Principal Component Analysis,PCA):是一种线性降维算法,计算速度快,但是难以反映数据内部的非线性关系。BROCKMAN、SnapATAC和Cusanovich2018都采用了PCA。但是只用PCA会造成大量细胞之间具有很高的相似性,因为每个细胞的剖面(Profile)中都含有大量的零值。因此,PCA通常与非线性降维算法一起使用。
- HTML file summarizing data & analysis: /home/jdoe/runs/sample345/outs/web_summary.html- Bed file of all called peak locations: /home/jdoe/runs/sample345/outs/peaks.bed- Raw peak barcode matrix in hdf5 format: /home/jdoe/runs/sample345/outs/raw_peak_bc_matrix.h5- Raw peak barcode ...
="filtered")# Perform standard analysis of each modality independently RNA analysispbmc.rna<-NormalizeData(pbmc.rna)pbmc.rna<-FindVariableFeatures(pbmc.rna)pbmc.rna<-ScaleData(pbmc.rna)pbmc.rna<-RunPCA(pbmc.rna)pbmc.rna<-RunUMAP(pbmc.rna,dims=1:30)# ATAC analysis add gene annotation ...