The winning methods for predicting cellular position in the DREAM single cell transcriptomics challenge

MotivationPredicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM Challenge on Single Cell Transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single cell transcriptomic data.ResultsWe have developed over 50 pipelines by combining different ways of pre-processing the RNA-seq data, selecting the genes, predicting the cell locations, and validating predicted cell locations, resulting in the winning methods for two out of three sub-challenges in the competition. In this paper, we present anRpackage,SCTCwhatateam, which includes all the methods we developed and theShinyweb-application to facilitate the research on single cell spatial reconstruction. All the data and the example use cases are available in the Supplementary material.AvailabilityThe scripts of the package are available athttps://github.com/thanhbuu04/SCTCwhatateamand theShinyapplication is available athttps://github.com/pvvhoang/SCTCwhatateam-ShinyAppContactThuc.Le@unisa.edu.auSupplementary informationSupplementary data are available atBriefings in Bioinformaticsonline.