ELF: Extract Landmark Features By Optimizing Topology Maintenance, Redundancy, and Specificity

scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq

Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilitating the detection of cell type-specific marker genes. In scRNA-seq experiments with multiple donors, the population level variation brings an extra layer of complexity in cell type-specific gene detection, for example, they may not appear in all donors. Motivated by this observation, we develop a statistical model named scCTS to identify cell type-specific genes from population-level scRNA-seq data. Extensive data analyses demonstrate that the proposed method identifies more biologically meaningful cell type-specific genes compared to traditional methods.

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

Accurate identification of cell types from single-cell RNA sequencing (scRNA-seq) data plays a critical role in a variety of scRNA-seq analysis studies. This task corresponds to solving an unsupervised clustering problem, in which the similarity measurement between cells affects the result significantly. Although many approaches for cell type identification have been proposed, the accuracy still needs to be improved. In this study, we proposed a novel single-cell clustering framework based on similarity learning, called SSRE. SSRE models the relationships between cells based on subspace assumption, and generates a sparse representation of the cell-to-cell similarity. The sparse representation retains the most similar neighbors for each cell. Besides, three classical pairwise similarities are incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE. Tested on ten real scRNA-seq datasets and five simulated datasets, SSRE achieved the superior performance in most cases compared to several state-of-the-art single-cell clustering methods. In addition, SSRE can be extended to visualization of scRNA-seq data and identification of differentially expressed genes. The matlab and python implementations of SSRE are available at https://github.com/CSUBioGroup/SSRE.

A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data

Background

Single-cell RNA sequencing (scRNAseq) data always involves various unwanted variables, which would be able to mask the true signal to identify cell-types. More efficient way of dealing with this issue is to extract low dimension information from high dimensional gene expression data to represent cell-type structure. In the past two years, several powerful matrix factorization tools were developed for scRNAseq data, such as NMF, ZIFA, pCMF and ZINB-WaVE. But the existing approaches either are unable to directly model the raw count of scRNAseq data or are really time-consuming when handling a large number of cells (e.g. n>500).

Results

In this paper, we developed a fast and efficient count-based matrix factorization method (single-cell negative binomial matrix factorization, scNBMF) based on the TensorFlow framework to infer the low dimensional structure of cell types. To make our method scalable, we conducted a series of experiments on three public scRNAseq data sets, brain, embryonic stem, and pancreatic islet. The experimental results show that scNBMF is more powerful to detect cell types and 10 - 100 folds faster than the scRNAseq bespoke tools.

Conclusions

In this paper, we proposed a fast and efficient count-based matrix factorization method, scNBMF, which is more powerful for detecting cell type purposes. A series of experiments were performed on three public scRNAseq data sets. The results show that scNBMF is a more powerful tool in large-scale scRNAseq data analysis. scNBMF was implemented in R and Python, and the source code are freely available at https://github.com/sqsun.