documentation for sc-type

[cathalgking]

I would like to use this package but it is quite poorly documented I find. The abstract on the paper says that it is an R package but I do not find instructions anywhere on how to install it? usually there is an install.packages() command
Is it necessary to load the source files with this in the R folder?
What databases are available to use with this package? What is the ''# example scRNA-seq matrix'' that is required? How can someone use another database for annotation (if possible) and can sc-type connect to any public databases? for example the MCA (Mouse cell atlas).

The web tool is poor too. I upload a SCE object that already has mt genes removed but now I am waiting ~10 mins for it to do this and normalise. Is it possible to interact with a Seurat object? if not, specify.

[IanevskiAleksandr]

Dear @cathalgking,

Did you manage to run the minimal reproducible example at the quick start here: https://github.com/IanevskiAleksandr/sc-type?

You don't need to install the package just run it directly by loading package functions (as shown in the quick start):

# load libraries and functions lapply(c("dplyr","Seurat","HGNChelper","openxlsx"), library, character.only = T) source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/gene_sets_prepare.R"); source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/sctype_score_.R")

By default, we use our in-built cell marker DB, however, feel free to use your own data. Just prepare an input XLSX file in the same format as our DB file. DB file should contain four columns (tissueType - tissue type, cellName - cell type, geneSymbolmore1 - positive marker genes, geneSymbolmore2 - marker genes not expected to be expressed by a cell type)

Hope this helps.
BR,
Aleksandr