基于以上需求,加拿大安大略省癌症研究所的研究人员设计了一个全面、泛癌的TME细胞类型分类工具scATOMIC(single cell annotation of tumour microenvironments in pan-cancer settings),通过反向层次分类和父节点重复消除的算法(RHC-REP)改进细胞分类,降低 TME 多细胞系统的转录组复杂性,对恶性和非恶性细胞进行模块化注释。
Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods req...
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...
Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA-seq data. Such methods are labor-intensive and heavily rely on user expertise, which may lead to inconsistent results. We present SCSA, an automatic tool to annotate cell types from single-ce...
Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed several automated cell type annotation tools, requiring neither biological knowledge nor subjective human decisions. Drop...
The ability to quantify differentiation potential of single cells is a task of critical importance. Here we demonstrate, using over 7,000 single-cell RNA-Seq profiles, that differentiation potency of a single cell can be approximated by computing the sig
更新程序如下:Algorithm分类中更新Heatmap、CircosHeatmap,SingleCell分类中更新FeatureQC, FeatureFilter, FeatureVariable, FeaturePCA, PCAJackStraw, CellUMAP, CellTSNE, MarkerViolin, MarkerUMAP, MarkerHeatmap, CellAnnotation。下面做简单介绍: Figure.1 BioSciTools-20230219 2.Algorithm New Apps 2.1 Heatmap ...
SCANPY: large-scale single-cell gene expression data analysis F. Alexander Wolf, Philipp Angerer, Fabian J. Theis Genome Biology2018 Feb 06. doi:10.1186/s13059-017-1382-0. You can cite the scverse publication as follows: The scverse project provides a computational ecosystem for single-cell...
The expanded, well-cleared brain enabled us to construct a point-based mouse brain atlas with single-cell annotation (CUBIC-Atlas). CUBIC-Atlas reflects inhomogeneous whole-brain development, revealing a significant decrease in the cerebral visual and somatosensory cortical areas during postnatal ...
In the field of machine learning, active and self-supervised learning methods have been proposed to improve the performance of a classifier while reducing both annotation time and label budget. However, the benefits of such strategies for single-cell annotation have yet to be evaluated in realistic...