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PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.

ABSTRACT: 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.

SUBMITTER: Papadopoulos N 

PROVIDER: S-EPMC6748774 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.

Papadopoulos Nikolaos N   Gonzalo Parra R PR   Söding Johannes J  

Bioinformatics (Oxford, England) 20190901 18

<h4>Summary</h4>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 th  ...[more]

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