Identifies stem cells among all detectable cell types within a population. StemID is an algorithm based on RaceID2 (Rare Cell Type Identification) an algorithm for the identification of rare and abundant cell types from single cell transcriptome data. The method is based on transcript counts obtained with unique molecular identifies. StemID is an algorithm for the derivation of cell lineage trees based on RaceID2 results and predicts multipotent cell identities.
Finds common and rare cell clusters in normal tissues and disease samples. GiniClust aims to simplify the study of single-cell data. It can be applied to data set coming from different platform, such as multiplex qPCR data, tranditional single cell RNAseq or UMI-based single cell RNAseq. This tool can be useful to annotate the Human Cell Atlas. It integrates information from complementary clustering methods.
Serves for single-cell data analysis. Granatum is a program that provides biologists with access to single-cell bioinformatics methods, and software developers with the opportunity to promote and combine their tools with various others in customizable pipelines. Its architecture simplifies the incorporation of cutting-edge tools and enables handling of large datasets. Moreover, it can eliminate inter-module incompatibilities by isolating the dependencies of each module.
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.
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