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GiniClust3: a fast and memory-efficient tool for rare cell type identification.

ABSTRACT:

Background

With the rapid development of single-cell RNA sequencing technology, it is possible to dissect cell-type composition at high resolution. A number of methods have been developed with the purpose to identify rare cell types. However, existing methods are still not scalable to large datasets, limiting their utility. To overcome this limitation, we present a new software package, called GiniClust3, which is an extension of GiniClust2 and significantly faster and memory-efficient than previous versions.

Results

Using GiniClust3, it only takes about 7?h to identify both common and rare cell clusters from a dataset that contains more than one million cells. Cell type mapping and perturbation analyses show that GiniClust3 could robustly identify cell clusters.

Conclusions

Taken together, these results suggest that GiniClust3 is a powerful tool to identify both common and rare cell population and can handle large dataset. GiniCluster3 is implemented in the open-source python package and available at https://github.com/rdong08/GiniClust3.

SUBMITTER: Dong R

PROVIDER: S-EPMC7183612 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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GiniClust3: a fast and memory-efficient tool for rare cell type identification.

Dong Rui R Yuan Guo-Cheng GC

BMC bioinformatics 20200425 1

<h4>Background</h4>With the rapid development of single-cell RNA sequencing technology, it is possible to dissect cell-type composition at high resolution. A number of methods have been developed with the purpose to identify rare cell types. However, existing methods are still not scalable to large datasets, limiting their utility. To overcome this limitation, we present a new software package, called GiniClust3, which is an extension of GiniClust2 and significantly faster and memory-efficient t ...[more]

PMID: 32334526

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