{ "_id": "6a12b047acfb0bcc41d19501", "Package": "scMappR", "Title": "Single Cell Mapper", "Version": "1.0.12", "Authors@R": "c(person(given = \"Dustin\", family = \"Sokolowski\", role = c(\"aut\", \"cre\"), email = \"djsokolowski95@gmail.com\"), person(given = \"Mariela\", family = \"Faykoo-Martinez\", role = \"aut\", email = \"mfaykoomartinez@gmail.com\"), person(given = \"Lauren\", family = \"Erdman\", role = \"aut\", email = \"lauren.erdman@sickkids.ca\"), person(given = \"Houyun\", family = \"Hou\", role = \"aut\", email = \"huayunhou@gmail.com\"), person(given = \"Cadia\", family = \"Chan\", role = \"aut\", email = \"cadia.chan@mail.utoronto.ca\"), person(given = \"Helen\", family = \"Zhu\", role = \"aut\", email = \"helen.m.zhu@gmail.com\"), person(given = \"Melissa\", family = \"Holmes\", role = \"aut\", email = \"melissa.holmes@utoronto.ca\"), person(given = \"Anna\", family = \"Goldenberg\", role = \"aut\", email = \"nyulik@gmail.com\"), person(given = \"Michael\", family = \"Wilson\", role = \"aut\", email = \"michael.wilson@sickkids.ca\"))", "Description": "The single cell mapper (scMappR) R package contains a\nsuite of bioinformatic tools that provide experimentally\nrelevant cell-type specific information to a list of\ndifferentially expressed genes (DEG). The function\n\"scMappR_and_pathway_analysis\" reranks DEGs to generate\ncell-type specificity scores called cell-weighted fold-changes.\nUsers input a list of DEGs, normalized counts, and a signature\nmatrix into this function. scMappR then re-weights bulk DEGs by\ncell-type specific expression from the signature matrix,\ncell-type proportions from RNA-seq deconvolution and the ratio\nof cell-type proportions between the two conditions to account\nfor changes in cell-type proportion. With cwFold-changes\ncalculated, scMappR uses two approaches to utilize\ncwFold-changes to complete cell-type specific pathway analysis.\nThe \"process_dgTMatrix_lists\" function in the scMappR package\ncontains an automated scRNA-seq processing pipeline where users\ninput scRNA-seq count data, which is made compatible for\nscMappR and other R packages that analyze scRNA-seq data. We\nfurther used this to store hundreds up regularly updating\nsignature matrices. The functions\n\"tissue_by_celltype_enrichment\", \"tissue_scMappR_internal\", and\n\"tissue_scMappR_custom\" combine these consistently processed\nscRNAseq count data with gene-set enrichment tools to allow for\ncell-type marker enrichment of a generic gene list (e.g. GWAS\nhits). Reference: Sokolowski,D.J., Faykoo-Martinez,M.,\nErdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A.\nand Wilson,M.D. (2021) Single-cell mapper (scMappR): using\nscRNA-seq to infer cell-type specificities of differentially\nexpressed genes. NAR Genomics and Bioinformatics. 3(1).\nIqab011. .", "License": "GPL-3", "URL": "", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "Packaged": { "Date": "2026-05-24 07:51:51 UTC", "User": "root" }, "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Author": "Dustin Sokolowski [aut, cre], Mariela Faykoo-Martinez [aut],\nLauren Erdman [aut], Houyun Hou [aut], Cadia Chan [aut], Helen\nZhu [aut], Melissa Holmes [aut], Anna Goldenberg [aut], Michael\nWilson [aut]", "Maintainer": "Dustin Sokolowski ", "Config/pak/sysreqs": "cmake libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3\nzlib1g-dev", "Repository": "https://dsokolo.r-universe.dev", "Date/Publication": "2025-06-25 17:10:02 UTC", "RemoteUrl": "https://github.com/cran/scMappR", "RemoteRef": "HEAD", "RemoteSha": "bb8ac09ba4f5500f4f29bffc40fa11bcd06444a9", "MD5sum": "b13c13b27b4a5ff9c967332ab53cff56", "_user": "dsokolo", "_type": "src", "_file": 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