PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes
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DOI：
10.1093/bioinformatics/btz078
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发表时间：
2019-09-15
期刊：
影响因子：
5.8
通讯作者：
Soeding, Johannes
中科院分区：
文献类型：
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作者：
Papadopoulos, Nikolaos;Gonzalo, Parra R.;Soeding, Johannes
细胞谱系树可以从分化细胞的单细胞RNA测序快照中获得。目前，只有具有简单拓扑的数据集可用。为了测试和进一步开发谱系树重建工具，我们需要测试具有已知复杂拓扑的数据集。PROSSTT可以模拟scRNA-seq数据集，用于具有任何所需复杂性、噪声水平、噪声模型和大小的谱系树的分化过程。PROSSTT还提供脚本来量化预测谱系树的质量。
A Summary: Cellular lineage trees can be derived from single-cell RNA sequencing snapshots of differentiating cells. Currently, only datasets with simple topologies are available. To test and further develop tools for lineage tree reconstruction, we need test datasets with known complex topologies. PROSSTT can simulate scRNA-seq datasets for differentiation processes with lineage trees of any desired complexity, noise level, noise model and size. PROSSTT also provides scripts to quantify the quality of predicted lineage trees.