spatialLIBD

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Thanks for the nice package! I've been using `vis_grid_clus` to plot multiple samples together. I noticed the legends representing levels of `clustervar` are always turning to numbers instead of showing...

boyiguo1

upload multiple Visium samples to the spatialLIBD shiny app

3

Maybe this is already possible? But I have 6 10x Visium datasets that I would like to upload to 1 shiny app for data mining and sharing. If possible, would...

cathalgking

Add support for non-Visium data and/or SpatialFeatureExperiment

3

Right now `spatialLIBD` is built upon the `SpatialExperiment` container class. There is also https://bioconductor.org/packages/SpatialFeatureExperiment/ that can support non-Visium spatially-resolved data. As new technologies come online, we will see which container...

lcolladotor

[Feature Request] registration_wrapper(): create and check validity of eventual pseudobulk factor names before starting

3

I recently ran registration_wrapper() on a very high-dimension dataset (~80 or ~200 clusters across 47 samples, depending on the granularity) and twice had runs go >8 hours before seeing warnings...

berniejmulvey

Error in loading app locally

1

I am using the example data in the documentation and I am not able to run the app locally. I am getting the following error when i use run_app() or...

dimurali93

[BUG] Error during extract and reformat enrichment results when using `registration_wrapper`

3

## Describe the bug Thanks for creating and maintaining the awesome `spatialLIBD` package. Recently, I was trying to conduct spatial registration by running `registration_wrapper` function on a `SpatialExperiment` object. I...

boyiguo1

We want to use `rlang` and `cli` to improve the user experience. See https://lcolladotor.github.io/jhustatcomputing2023/posts/18-debugging-r-code/#errors-%C3%A0-la-tidyverse for a quick intro into how these functions improve error messages.

lcolladotor

Translate to Spanish the short workshop #68 and other intro level materials to help increase access to these technologies to Spanish-speaking individuals. This will help increase diversity of our user...

lcolladotor

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...

lcolladotor

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...

lcolladotor