scMappR: 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).

Version: 0.1.1
Depends: R (≥ 3.6.0)
Imports: ggplot2, pheatmap, graphics, Seurat, GSVA, stats, utils, downloader, pcaMethods, grDevices, gProfileR, limSolve, gprofiler2
Suggests: testthat, knitr, rmarkdown
Published: 2020-03-05
Author: Dustin Sokolowski [aut, cre], Mariela Faykoo-Martinez [aut], Michael Wilson [aut], Anna Goldenberg [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski at sickkids.ca>
License: GPL-3
NeedsCompilation: no
Materials: README
CRAN checks: scMappR results

Downloads:

Reference manual: scMappR.pdf
Vignettes: single cell Mapper (scMappR)
Package source: scMappR_0.1.1.tar.gz
Windows binaries: r-devel: scMappR_0.1.1.zip, r-release: scMappR_0.1.1.zip, r-oldrel: scMappR_0.1.1.zip
macOS binaries: r-release: scMappR_0.1.1.tgz, r-oldrel: scMappR_0.1.1.tgz
Old sources: scMappR archive

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