PROSSTT：用于复杂分化过程的单细胞 RNA-seq 数据的概率模拟。
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.
机构信息
Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
出版信息
Bioinformatics. 2019 Sep 15;35(18):3517-3519. doi: 10.1093/bioinformatics/btz078.
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.
AVAILABILITY AND IMPLEMENTATION
https://github.com/soedinglab/prosstt.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
细胞谱系树可从分化细胞的单细胞 RNA 测序快照中得出。目前，仅提供具有简单拓扑结构的数据集。为了测试和进一步开发谱系树重建工具，我们需要具有已知复杂拓扑结构的测试数据集。PROSSTT 可以模拟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 scRNA-seq 数据集。PROSSTT 还提供了用于量化预测谱系树质量的脚本。
可用性和实现
https://github.com/soedinglab/prosstt。
补充信息
补充数据可在“Bioinformatics”在线获取。
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