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: | 0.1.3 |
| Depends: | R (≥ 4.0.0) |
| Imports: | ggplot2, pheatmap, graphics, Seurat, GSVA, stats, utils, downloader, pcaMethods, grDevices, gProfileR, limSolve, gprofiler2, pbapply |
| Suggests: | testthat, knitr, rmarkdown |
| Published: | 2020-07-20 |
| 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 |
| Reference manual: | scMappR.pdf |
| Vignettes: |
single cell Mapper (scMappR) |
| Package source: | scMappR_0.1.3.tar.gz |
| Windows binaries: | r-devel: scMappR_0.1.3.zip, r-release: scMappR_0.1.3.zip, r-oldrel: scMappR_0.1.1.zip |
| macOS binaries: | r-release: scMappR_0.1.3.tgz, r-oldrel: scMappR_0.1.1.tgz |
| Old sources: | scMappR archive |
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