SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data
Abstract Quality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that datasets are comprised of one cell type, potentially resulting in biased exclusion of rare cell types. We introduce SampleQC, which robustly...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-02859-3 |
| _version_ | 1811165857619902464 |
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| author | Will Macnair Mark Robinson |
| author_facet | Will Macnair Mark Robinson |
| author_sort | Will Macnair |
| collection | DOAJ |
| description | Abstract Quality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that datasets are comprised of one cell type, potentially resulting in biased exclusion of rare cell types. We introduce SampleQC, which robustly fits a Gaussian mixture model across multiple samples, improves sensitivity, and reduces bias compared to current approaches. We show via simulations that SampleQC is less susceptible to exclusion of rarer cell types. We also demonstrate SampleQC on a complex real dataset (867k cells over 172 samples). SampleQC is general, is implemented in R, and could be applied to other data types. |
| first_indexed | 2024-04-10T15:44:20Z |
| format | Article |
| id | doaj.art-8b268e80edcc45ecae31ce50cb52d616 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-10T15:44:20Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-8b268e80edcc45ecae31ce50cb52d6162023-02-12T12:13:43ZengBMCGenome Biology1474-760X2023-02-0124112210.1186/s13059-023-02859-3SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell dataWill Macnair0Mark Robinson1Department of Molecular Life Sciences, University of ZürichDepartment of Molecular Life Sciences, University of ZürichAbstract Quality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that datasets are comprised of one cell type, potentially resulting in biased exclusion of rare cell types. We introduce SampleQC, which robustly fits a Gaussian mixture model across multiple samples, improves sensitivity, and reduces bias compared to current approaches. We show via simulations that SampleQC is less susceptible to exclusion of rarer cell types. We also demonstrate SampleQC on a complex real dataset (867k cells over 172 samples). SampleQC is general, is implemented in R, and could be applied to other data types.https://doi.org/10.1186/s13059-023-02859-3Single cellSingle-cell RNA-seqQuality control |
| spellingShingle | Will Macnair Mark Robinson SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data Genome Biology Single cell Single-cell RNA-seq Quality control |
| title | SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data |
| title_full | SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data |
| title_fullStr | SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data |
| title_full_unstemmed | SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data |
| title_short | SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data |
| title_sort | sampleqc robust multivariate multi cell type multi sample quality control for single cell data |
| topic | Single cell Single-cell RNA-seq Quality control |
| url | https://doi.org/10.1186/s13059-023-02859-3 |
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