(2012). Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS ONE 7, e41374.Chen H, Tian Y, Shu W, Bo X, Wang S: Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding...
We describe Garnett, a tool for rapidly annotating cell types in single-cell transcriptional profiling and single-cell chromatin accessibility datasets, based on an interpretable, hierarchical markup language of cell type-specific genes. Garnett successfully classifies cell types in tissue and whole ...
Recent advances in single-cell technologies have enabled the characterization of epigenomic heterogeneity at the cellular level. Computational methods for automatic cell type annotation are urgently needed given the exponential growth in the number of ce
Recent advances in single-cell technologies have enabled the characterization of epigenomic heterogeneity at the cellular level. Computational methods for automatic cell type annotation are urgently needed given the exponential growth in the number of cells. In particular, annotation of single-cell chromati...
Aran, Looney, Liu et al. Reference-basedanalysis of lung single-cell sequencing reveals a transitional profibroticmacrophage. Nature Immunology (2019) SingleR是一个用于对单细胞RNA-seq测序(scRNA-seq)数据进行细胞类型自动注释的R包(Aran et al.2019),是基于表达值的correlation的。它通过给定的具有已知类型...
#class:SingleCellExperiment #dim:33694737280 参考数据集:celldex包提供的BlueprintEncodeData() The Blueprint/ENCODE reference consists of bulk RNA-seq data for pure stroma and immune cells generated by Blueprint (Martens and Stunnenberg 2013) and ENCODE projects (The ENCODE Project Consortium 2012)....
OSCA单细胞数据分析笔记11—Celltypeannotation OSCA单细胞数据分析笔记11—Celltypeannotation “物以类聚”的类是什么类？⽐如将⼀群⽔果分为不同的类群，则⼜红⼜圆特征的可能是苹 果。对于单细胞聚类的结果，类的最直接注释就是细胞类型。本节将学习单细胞数据分析 过程中注释细胞类型的三种思路。笔记...
coupled electron transport BP 52 7 9.225569e-08# GO:0046390 ribose phosphate biosynthetic process BP 147 10 1.203158e-07# GO:0022408 negative regulation of cell-cell adhesion BP 187 11 1.225564e-07# GO:0009152 purine ribonucleotide biosynthetic process BP 131 9 4.817966e-07# GO:0035148 tube ...
The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partially...
“Celltype”: The predicted celltype name. “Score” : The predicted score for a celltype normalized by Z-score method. “nan” will be assigned if only one celltype found. “Times” : The score of the first predicted celltype / The score of the second predicted celltype ...