SNPRelate 1.34.1 is an R package for directly computing distance matrices between samples from VCF files, building kinship trees or performing hierarchical clustering. Its main purpose is to provide convenient and fast functions to help users quickly generate kinship trees or cluster analysis results from sequence data.
Single Cell RNA Sequencing (scRNA-seq) can reveal the heterogeneity of gene expression in single cells. However, this technique faces a common problem, that is, the interference of doublets. Double cells are mixtures of RNA from two or more different cells, the presence of which can lead to inaccurate interpretation of gene expression. Therefore, we can use the DoubletFinder suite to remove these double cells to obtain more accurate and cleaner scRNA-seq data.
scCATCH is an R suite that automatically annotates cell types, including at least 353 cell types, 686 cell subtypes, and 2096 human and mouse cell type references. This article introduces the usage and operation process of scCATCH in detail.
Subclustering cell populations is a common step in the study of single-cell data. This article shares analysis steps and methods for specific cell populations and provides example data.
This article will introduce how to use Seurat to analyze single-cell data, including how to extract specific cells, name and calculate percentages, etc., with sample data for reference.
Batch effects are a common problem in the analysis of single-cell data and can lead to misinterpretation of differences between samples. The Seurat Integration method can be used to solve data integration and transfer problems.
The kit for automatic identification of cells can only be used for preliminary identification of cell types. If you want to further confirm the cell type, you need to rely on the knowledge and experience of the researcher for judgment. The following are some commonly used cell marker databases for single-cell data analysis. The methods of use are very simple. You only need to input the name of the characteristic gene, and you can find the possible corresponding cells from the database for your reference.
A tool for automatic annotation of single-cell cell types
Clustree is an R-based suite for visualizing the structure and hierarchy of clustering trees. The suite provides a simple and intuitive way for researchers to visually explore the results of cluster analysis.
