spatialLIBD
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LieberInstitute
Code for the spatialLIBD R/Bioconductor package and shiny app
https://github.com/clauswilke/colorblindr has great utilities for simulating visual impairments. It is not available on CRAN or Bioconductor, which means that we cannot use it as-is in `spatialLIBD`. However, we want to...
We want to enable users to write their own custom `shiny` code for the web applications that can be provided as an extra tab. We will create a new guide...
Using on-disk memory representations like HDF5 files as well as remotely-hosted images supported by `SpatialExperiment`, we should explore the limits for dataset sizes that are can be hosted on shinyapps.io....
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...
Related to #62, we can also expand the interactive web applications by adding support for visualization tools such as `escheR` https://bioconductor.org/packages/escheR/ that can help users when visualizing multiple variables in...
The code for the `shiny` interactive web applications needs to be modularized and broken up into smaller units. One framework for doing so is the `golem` and `golemverse` framework https://golemverse.org/....
Currently https://research.libd.org/spatialLIBD/reference/frame_limits.html is limited to dimensions in Visium capture areas. We know that Visium HD will likely be larger. Also, the current function is slow and we should improve the...
As discussed at https://github.com/LieberInstitute/spatialLIBD/issues/49#issuecomment-1721830412, we want to add support for `dream()` in the spatial registration functions. We also want to maintain backward compatibility with the `limma`-based options we have currently...
Create a fully complete and step by step guide for deploying `spatialLIBD` apps on shinyapps.io. While this is partially documented, the current information is not enough for users who are...
We want to refactor https://research.libd.org/spatialLIBD/articles/TenX_data_download.html to make it more user friendly. The current organization and level of detail can be confusing for new users. Currently, it follows the order in...
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Code for the spatialLIBD R/Bioconductor package and shiny app