Improve data access organization and documentation

[lcolladotor]

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.

[lahuuki]

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]

[lahuuki]

sce_example is a single cell experiment that contains spaital data

sce <- fetch_data("sce_example")
# snapshotDate(): 2025-04-12
# 2025-06-09 20:22:04.489006 loading file /Users/louise.huuki/Library/Caches/org.R-project.R/R/BiocFileCache/bb6440b4c464_sce_sub_for_vignette.Rdata%3Fdl%3D1
colData(sce)
# DataFrame with 47681 rows and 74 columns
#                             barcode sample_name   tissue       row       col  imagerow
#                            <factor>   <integer> <factor> <integer> <integer> <numeric>
# AAACAACGAATAGTTC-1 AAACAACGAATAGTTC-1      151507        1         0        16   113.141
# AAACAAGTATCTCCCA-1 AAACAAGTATCTCCCA-1      151507        1        50       102   383.438
# AAACAATCTACTAGCA-1 AAACAATCTACTAGCA-1      151507        1         3        43   129.523
# AAACACCAATAACTGC-1 AAACACCAATAACTGC-1      151507        1        59        19   431.188
# AAACAGCTTTCAGAAG-1 AAACAGCTTTCAGAAG-1      151507        1        43         9   344.869