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 |
| 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 |
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