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Makes analysis more broadly accessible to researchers. Granatum is a web browser based scRNAseq analysis pipeline that conveniently walks the users through various steps of scRNA-seq analysis. It has a comprehensive list of modules, including plate merging and batch effect removal, outlier sample removal, gene filtering, gene expression normalization, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell series construction.


Models transcriptional cell fates as mixtures of the Gaussian Process Latent Variable Model and Overlapping Mixtures of Gaussian Processes (OMGP). GPfates is based on first reconstructing the differentiation trajectory from the observed data, thereby establishing an order for the cells. In a second step, GPfates uses the inferred temporal orders as input for a nonparametric time series mixture model. This approach revealed two simultaneous trends emerging during pseudotime, which separated from each other, indicating that a developmental bifurcation occurred. In a third step, GPfates uses a change point model, thereby facilitating to annotate pseudotime after bifurcation. The source code is freely available for download.