Recherche
An algorithm to automatise marker-based purification of specific cell populations
Carmona Lab develops scGate, an intuitive tool to purify a cell population of interest from complex scRNA-seq datasets based on literature-derived marker genes.
scGate is implemented as an R package and integrated with the Seurat framework, providing an intuitive tool to isolate cell populations of interest from heterogeneous single cell datasets.
The project* was led by Massimo Andreatta and Santiago Carmona, in collaboration with Ariel Berenstein of the Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, Buenos Aires. Its results are published in Bioinformatics.
R package source code and reproducible tutorials are available at Github.
The research was supported by the Swiss National Science Foundation (SNSF) Ambizione programme.
* scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets