SSBER: removing batch effect for single-cell RNA sequencing data
| Autor: | Fei Wang, Yin Zhang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Computer science
QH301-705.5 Population Sequencing data Computer applications to medicine. Medical informatics R858-859.7 Supervised cell type assignment Batch effect computer.software_genre Biochemistry 03 medical and health sciences 0302 clinical medicine Structural Biology Exome Sequencing Biology (General) education Molecular Biology 030304 developmental biology 0303 health sciences education.field_of_study Cell type composition Sequence Analysis RNA The shared cell type Applied Mathematics Methodology Article Computer Science Applications Transcriptome Sequencing RNA Data integration Single-Cell Analysis Biological system Transcriptome computer 030217 neurology & neurosurgery Algorithms |
| Zdroj: | BMC Bioinformatics, Vol 22, Iss 1, Pp 1-20 (2021) BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | Background With the continuous maturity of sequencing technology, different laboratories or different sequencing platforms have generated a large amount of single-cell transcriptome sequencing data for the same or different tissues. Due to batch effects and high dimensions of scRNA data, downstream analysis often faces challenges. Although a number of algorithms and tools have been proposed for removing batch effects, the current mainstream algorithms have faced the problem of data overcorrection when the cell type composition varies greatly between batches. Results In this paper, we propose a novel method named SSBER by utilizing biological prior knowledge to guide the correction, aiming to solve the problem of poor batch-effect correction when the cell type composition differs greatly between batches. Conclusions SSBER effectively solves the above problems and outperforms other algorithms when the cell type structure among batches or distribution of cell population varies considerably, or some similar cell types exist across batches. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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