Leonardo Collado-Torres
Leonardo Collado-Torres
We want to create a collection of short videos (likely shared on YouTube) demonstrating how to use the different features of the `spatialLIBD` interactive websites. We will collate these videos...
Develop a long format workshop to teach in 2 days the basics of spatially-resolved transcriptomics analysis using `spatialLIBD`. We might want to learn about the format used by https://carpentries.org/index.html for...
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...