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Gene sets with weights trained from the PBMC 3k dataset

hitypedb_pbmc3k.Rd

Marker gene sets for the 9 cell types of the Seurat PBMC 3k tutorial (Naive CD4+ T, CD14+ Mono, Memory CD4+, B, CD8+ T, FCGR3A+ Mono, NK, DC and Platelet), with weights trained on the dataset itself. It is intended for demonstration: pass it to gs_prepare like any other marker data frame (e.g. gs_prepare(hitypedb_pbmc3k)).

Usage

hitypedb_pbmc3k

Format

A data frame in the marker database format used by gs_prepare: cellName, geneSymbolmore1, geneSymbolmore2 and level, where geneSymbolmore1 carries +/- suffixes encoding the trained weights.

Source

Trained with train_weights on the PBMC 3k dataset (Seurat guided-clustering tutorial, resolution 0.5).