scMappR: Single Cell Mapper

The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.

Version:	1.0.11
Depends:	R (≥ 4.0.0)
Imports:	ggplot2, pheatmap, graphics, Seurat, GSVA, stats, utils, downloader, pcaMethods, grDevices, gProfileR, limSolve, gprofiler2, pbapply, ADAPTS, reshape
Suggests:	testthat, knitr, rmarkdown
Published:	2023-06-30
DOI:	10.32614/CRAN.package.scMappR
Author:	Dustin Sokolowski [aut, cre], Mariela Faykoo-Martinez [aut], Lauren Erdman [aut], Houyun Hou [aut], Cadia Chan [aut], Helen Zhu [aut], Melissa Holmes [aut], Anna Goldenberg [aut], Michael Wilson [aut]
Maintainer:	Dustin Sokolowski <djsokolowski95 at gmail.com>
License:	GPL-3
NeedsCompilation:	no
Materials:	README
CRAN checks:	scMappR results

Documentation:

Reference manual:	scMappR.pdf
Vignettes:	single cell Mapper (scMappR)

Downloads:

Package source:	scMappR_1.0.11.tar.gz
Windows binaries:	r-devel: scMappR_1.0.11.zip, r-release: scMappR_1.0.11.zip, r-oldrel: scMappR_1.0.11.zip
macOS binaries:	r-release (arm64): scMappR_1.0.11.tgz, r-oldrel (arm64): not available, r-release (x86_64): scMappR_1.0.11.tgz, r-oldrel (x86_64): not available
Old sources:	scMappR archive

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