Leonardo Collado-Torres

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...

As `spatialLIBD` lists provides access to several datasets through Dropbox, we want to upgrade this and provide access to the datasets through ExperimentHub by Bioconductor.

Based on the spatialDLPFC project, we decided that the heatmaps look better when made with `ComplexHeatmap`. We need to change all internal heatmaps to use this package.

Born from the NAc project, we want to add support for visualizing multiple capture areas that have been stitched together.

Improve internal code coverage using `covr` from the current 6% to at least 75% or higher for non-interactive functions.

expressed_regions() is not working with the new IDIES and AWS bigWig file locations

5

Hi, Currently in BioC release (3.16) and devel (3.17), `recount` is failing. That's because neither the new IDIES location nor AWS are allowing us to read the BigWig files from...

Openssl is not available in netConnectHttps for importing remote BigWig files

7

Hi, I'm having trouble importing remote BigWig files with `derfinder`, [which internally](https://github.com/lcolladotor/derfinder/blob/5c1cbd412c5787bf2d2d778977e38dd6ae64976d/R/loadCoverage.R#L400) uses `rtracklayer::import()`. I noticed this when looking at `recount` which is failing on BioC 3.16 and 3.17 (details...

tracks(xlim) doesn't work with GRanges input

3

Hi, `derfinderPlot::plotCluster()` is currently failing https://bioconductor.org/checkResults/release/bioc-LATEST/derfinderPlot/nebbiolo2-buildsrc.html and I traced it back to `ggbio`. Here's a small reproducible example that shows that `tracks(xlim)` fails if you pass it a `GRanges` object....

GitHub actions and styler suggestions

1

Hi, Based on my recent work for https://github.com/r-lib/actions/issues/84, I want to make a few small PRs to the BioC website. The feasibility of the PRs for the Bioc website also...