The increasing amount of time-series single-cell RNA sequencing (scRNA-seq) data raises the key issue of connecting cell states (i.e. cell clusters or cell types) to obtain the continuous temporal dynamics of transcription, which can highlight the unified biological mechanisms involved in cell state transitions. However, most existing trajectory methods are specifically designed for individual cells, so they can hardly meet the needs of accurately inferring the trajectory topology of the cell state, which usually contains cells assigned to different branches.


Here, we present CStreet, a computed Cell State trajectory inference method for time-series scRNA-seq data. It uses time-series information to construct the k-nearest neighbor connections between cells within each time point and between adjacent time points. Then, CStreet estimates the connection probabilities of the cell states and visualizes the trajectory, which may include multiple starting points and paths, using a force-directed graph. By comparing the performance of CStreet with that of six commonly used cell state trajectory reconstruction methods on simulated data and real data, we demonstrate the high accuracy and high tolerance of CStreet.

Availability and implementation

CStreet is written in Python and freely available on the web at and

Supplementary information

Supplementary data are available at Bioinformatics online.

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