Single Cell Mapper

Statistical tools to interrogate the cell-type specificity of any gene list given a matrix of cell-types and genes associated with those cell-types (a signature matrix). Additionally, a library of over 245 signature matrices from public data are stored. Together, there are four primary functions: (i) processing scRNA-seq count data and automated cell-type naming using 'Seurat' V3 and enrichment of CellMarker and Panglao databases, (ii) tissue-by-cell-type gene set enrichment, (iii) cell-type specific enrichment of a gene list within a particular tissue, (iv) weighted cell-type specific reranking of a list of differentially expressed genes. Reference: Sokolowski DJ, Faykoo-Martinez M, Erdman L, Hou H, Uuskula-Reimand L, Yuki K, Zhu H, Goldenberg A, Wilson MD (In Preparation).


Reference manual

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0.1.1 by Dustin Sokolowski, 4 months ago

Browse source code at

Authors: Dustin Sokolowski [aut, cre] , Mariela Faykoo-Martinez [aut] , Michael Wilson [aut] , Anna Goldenberg [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports ggplot2, pheatmap, graphics, Seurat, GSVA, stats, utils, downloader, pcaMethods, grDevices, gProfileR, limSolve, gprofiler2

Suggests testthat, knitr, rmarkdown

See at CRAN