single-cell mapper (scMappR) data repository

Dustin Sokolowski: dustin-dot-sokolowski-at-sickkids-dot-ca

Date: 09/28/2020

Description

Primary utility of the scMappR_Data R package.

This repository complements the primary scMappR package by providing all of the data files required to run the different analyses in scMappR. Every function within the main package has a rda_path parameter. This parameter allows users to set where the scMappR_Data package is downloaded in their local machine. If the scMappR_Data pacakge is not downloaded and a file is required, then scMappR will temporarily download and load that file into R using the downloader R package.

Primary function of scMappR

Description of scMappR R package adapted from pre-print. 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 (cwFold-change). cwFold-changes are the original fold-changes identified with bulk differential analysis that are then scaled by the cell-type specificity of the DEG and the cell-type proportion of the inputted samples.

"PBMC_scMappR_and_pathway_analysis_example.rda"

The "PBMC_scMappR_and_pathway_analysis_example.rda" file loads the PBMC_example object of class "list". This file contains the sex differences, signature matrix, and normalized bulk RNA-seq matrix from the Monaco et al., 2019 study (Figure 3 of the main figure).

• bulk_DE_cors: Gene, adjusted P-value, and Log2FC
• bulk_normalized: CPM normalized counts.
• odds_ratio_in: signature matrix of different immune cell-types.

"Preoptic_region_example.rda"

The "Preoptic_region_example.rda" file loads the POA_example of class "list". This file contains the cell-type markers, p-value signature matrix, and odds-ratio signature matrix of a Pre-optic area scRNA-seq dataset (Moffitt et al., 2018).

• POA_generes: A list of cell-type markers as an output of the FindMarkers function in Seurat.
• POA_OR_signature: The signature matrix of the fold-changes generated from the 2^(avg_logFC)*sign(ave_logFC) of cell-type markers.
• POA_OR_signature: The signature matrix of the ranks generated from the -1*log10(p_val_adj)*sign(p_val_adj) of cell-type markers.

"Signature_matrices_OR.rda"

The "Signature_matrices_OR.rda" file loads the OddsRatioSignature of class "list". This file contains the fold-change signature matrices of all pre-processed scRNA-seq datasets.

"Signature_matrices_Pval.rda"

The "Signature_matrices_Pval.rda" file loads the RankValueSignature of class "list". This file contains the fold-change signature matrices of all pre-processed scRNA-seq datasets.

"Signature_matrices_cellLabel.rda"

The "Signature_matrices_cellLabel.rda" file loads the celltypeLabels of class "list". This file contains the top (up-to) 30 cell-type markers and estimated cell-type labels from the CellMarker and Panglao datasets using the Fisher's exact test and GSVA methods.

"TopGenes.rda"

The "TopGenes.rda" file loads the TopGenesList of class "list". This file contains the cell-type markers from each study, tissue, and cell-type.

"bioMart_ortholog_human_mouse.rda"

The "bioMart_ortholog_human_mouse.rda" file loads the bioMart_orthologs of class "data.frame". This file contains the 1-1 orthologs between mouse and human gene symbols.

"cell_preferences_categorized.rda

The "cell_preferences_categorized.rda" file loads the cell_preference_final of class "list". This file contains 14 tissue categories. If a researcher chooses one of the available cell-type labelling methods (e.g. brain). Then scMappR will pick labels from this category.

"cell_process_example.rda"

The "cell_process_example.rda" file loads the sm of class "dgCMatrix". This file contains a matrix of 22k genes and 500 cells from scRNA-seq retinal data. This is to work with the process_dgTMatrix_lists.

"do_valle_duraes_2020_rnaseq.rda"

The "do_valle_duraes_2020_rnaseq.rda" file loads the do_valle_duraes_2020_rnaseq of class "list".

• counts: raw counts of bulk kidney RNA-seq from do Valle Duraes 2020.
• phenotype: data frame of the sample information from the bulk kidney RNA-seq samples.
• Signature: a gene by cell-type matrix of the fold-change that a gene is in each cell-type. The signature matrix is from the Tabula Muris 2018 paper.

"human_cell_markers"

The "human_cell_markers" file loads the gmt_list object that will label cell-types (human gene symbols) from different sources.

• gmt_both: cell-type marker database from the CellMarker and PanglaoDB databases.
• gmt_cellmarker: cell-type marker database from the CellMarker database.
• gmt_panglao: cell-type marker database from the Panglao database.
• gmt_gobp: list of human gene ontologies.
• gmt_subtype: cell-type marker database of neurons specifically.

"mouse_cell_markers"

The "mouse_cell_markers" file loads the gmt_list object that will label cell-types (human gene symbols) from different sources.

• gmt_both: cell-type marker database from the CellMarker and PanglaoDB databases.
• gmt_cellmarker: cell-type marker database from the CellMarker database.
• gmt_panglao: cell-type marker database from the Panglao database.
• gmt_gobp: list of human gene ontologies.
• gmt_subtype: cell-type marker database of neurons specifically.

"human_tissue_celltype_scMappR.rda"

The "human_tissue_celltype_scMappR.rda": cell-type marker database of human gene symbols listing human cell-types.

"mouse_tissue_celltype_scMappR.rda"

The "mouse_tissue_celltype_scMappR.rda": cell-type marker database of mouse gene symbols listing mouse cell-types.