Dataset Information

ProgClust: A progressive clustering method to identify cell populations.

ABSTRACT: Identifying different types of cells in scRNA-seq data is a critical task in single-cell data analysis. In this paper, we propose a method called ProgClust for the decomposition of cell populations and detection of rare cells. ProgClust represents the single-cell data with clustering trees where a progressive searching method is designed to select cell population-specific genes and cluster cells. The obtained trees reveal the structure of both abundant cell populations and rare cell populations. Additionally, it can automatically determine the number of clusters. Experimental results show that ProgClust outperforms the baseline method and is capable of accurately identifying both common and rare cells. Moreover, when applied to real unlabeled data, it reveals potential cell subpopulations which provides clues for further exploration. In summary, ProgClust shows potential in identifying subpopulations of complex single-cell data.

SUBMITTER: Li H

PROVIDER: S-EPMC10115987 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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ProgClust: A progressive clustering method to identify cell populations.

Li Han H Wang Ying Y Lai Yongxuan Y Zeng Feng F Yang Fan F

Frontiers in genetics 20230406

Identifying different types of cells in scRNA-seq data is a critical task in single-cell data analysis. In this paper, we propose a method called ProgClust for the decomposition of cell populations and detection of rare cells. ProgClust represents the single-cell data with clustering trees where a progressive searching method is designed to select cell population-specific genes and cluster cells. The obtained trees reveal the structure of both abundant cell populations and rare cell populations. ...[more]

PMID: 37091787

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Project description:BackgroundPrevious studies from Ethiopia detected disease clustering using broader geographic settings, but limited information exists on the spatial distribution of the disease using residential locations. An assessment of predictors of spatial variations of TB at community level could fill the knowledge gaps, and helps in devising tailored interventions to improve TB control.ObjectiveTo assess the pattern of spatial distribution of pulmonary tuberculosis (PTB) based on geographic locations of individual cases in the Dale district and Yirga Alem town in southern Ethiopia.MethodsThe socio-demographic characteristics of PTB cases were collected using a structured questionnaire, and spatial information was collected using geographic position systems. We carried out Getis and Ord (Gi*) statistics and scan statistics to explore the pattern of spatial clusters of PTB cases, and geographically weighted regression (GWR) was used to assess the spatial heterogeneities in relationship between predictor variables and PTB case notification rates (CNRs).ResultsThe distribution of PTB varied by enumeration areas within the kebeles, and we identified areas with significant hotspots in various areas ineach year. In GWR analysis, the disease distribution showed a geographic heterogeneity (non-stationarity) in relation to physical access (distance to TB control facilities) and population density (AICc = 5591, R2 = 0.3359, adjusted R2 = 0.2671). The model explained 27% of the variability in PTB CNRs (local R2 ranged from 0.0002-0.4248 between enumeration areas). The GWR analysis showed that areas with high PTB CNRs had better physical accessibility to TB control facilities and high population density. The effect of physical access on PTB CNRs changed after the coverage of TB control facilities was improved.ConclusionWe report a varying distribution of PTB in small and different areas over 10 years. Spatial and temporal analysis of disease distribution can be used to identify areas with a high burden of disease and predictors of clustering, which helps in making policy decisions and devising targeted interventions.

Dataset Information

ProgClust: A progressive clustering method to identify cell populations.

Publications

ProgClust: A progressive clustering method to identify cell populations.

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