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lcolladotor opened this issue Nov 30, 2023 · 2 comments
Open

Improve data access organization and documentation #56

lcolladotor opened this issue Nov 30, 2023 · 2 comments
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enhancement New feature or request
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@lcolladotor
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Currently available datasets are specified as arguments to the fetch_data() function. The documentation can be improved and the available datasets can be reorganized. We need to re-design this and create a vignette documenting available datasets, list related publications, include abstracts of the available datasets, link to the project GitHub repositories, among other enhancements.

@lcolladotor lcolladotor added the enhancement New feature or request label Nov 30, 2023
@lcolladotor lcolladotor added this to the bioc v3.20 milestone Nov 30, 2023
@lcolladotor lcolladotor changed the title Improve data access Improve data access organization and documentation Nov 30, 2023
@lahuuki
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lahuuki commented Mar 13, 2025

Details to add about spatialDLPFC snRNA-seq data

#' ## exclude Ambigious cells
#' sce <- sce[, sce$cellType_hc != "Ambiguous"]
#' 
#' ## cellType_layer contains the final layer cell type annotations
#' table(sce$cellType_layer)
#' # Astro    EndoMural        Micro        Oligo          OPC   Excit_L2/3 
#' #  3979         2157         1601        10894         1940           82 
#' # Excit_L3 Excit_L3/4/5     Excit_L4     Excit_L5   Excit_L5/6     Excit_L6 
#' #    10459         3043         2388         2505         2487         1792 
#' # Excit_ambig        Inhib 
#' #        2053        11067 

@lahuuki
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lahuuki commented Mar 13, 2025

Image

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