Splatter: simulation of single-cell RNA sequencing data
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Cites methods from "Splatter: simulation of single-cell..."
...In order to examine the performance of Slingshot and other methods in a wide range of scenarios, we performed a simulation study using the Bioconductor R package splatter [28] to produce artificial single-cell RNA-Seq datasets....
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...In order to make a more quantitative comparison of different lineage inference methods and examine Slingshot’s robustness to upstream computational choices, we conducted a simulation study with synthetic datasets generated using the Bioconductor R package splatter [28]....
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1,180 citations
Cites background from "Splatter: simulation of single-cell..."
...We thus find significant marker genes even when clustering random data generated by splatter (Zappia et al, 2017) (see Appendix Supplementary Text S3)....
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1,148 citations
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928 citations
References
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"Splatter: simulation of single-cell..." refers background in this paper
...0) [41] and converted to a gene by cell matrix....
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30,684 citations
"Splatter: simulation of single-cell..." refers methods in this paper
...2a) [37], and counted reads overlapping genes in the Gencode V22 annotation using featureCounts (v1....
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29,504 citations
29,413 citations
"Splatter: simulation of single-cell..." refers methods in this paper
...The negative binomial is the most common distribution used to model RNA-seq count data, as in the edgeR [22] and DESeq [23] packages....
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...BCV parameters are estimated using the estimateDisp function in the edgeR package [22]....
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14,103 citations