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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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How to use spatialLIBD with other data #7

Closed lcolladotor closed 3 years ago

lcolladotor commented 3 years ago

We want to write a new vignette that shows how you can use spatialLIBD using the data from https://support.10xgenomics.com/spatial-gene-expression/datasets. I think that it can start with https://github.com/LieberInstitute/spatialDLPFC/blob/main/analysis/01_build_SPE.R but run a quick clustering algorithm like K-means (maybe using minibatchkmeans). The vignette should include the code from https://github.com/LieberInstitute/spatialDLPFC/blob/main/analysis/03_try_shiny.R as well.

With biocthis::use_bioc_vignette() we can start the new Rmd file.

In the future when https://github.com/HelenaLC/TENxVisiumData is on BioC, the vignette could show how to use it.

lcolladotor commented 3 years ago

This issue depends on #5 and to a lesser extent on #6.

lcolladotor commented 3 years ago

@abspangler13 and/or @bpardo99, do you want to give this a go? (#5 and the paper draft are higher priorities though)

lcolladotor commented 3 years ago

Resolved with version 1.3.12