Release Notes: Xenium Panel Designer

Incorporated NUPACK to enhance probe design. Panel designer now targets five probe sets per gene for Xenium Prime custom panels.
Updated BED files to show the codeword and probe set index for each entry.
Added "xenografts" to the Advanced target list on the "Tell us about your panel" page.
Added a probe details file (probe_info.csv.gz) to "Output files" table for completed panel designs.

Enabled design for Xenium Prime 5K human or mouse custom add-on panels. For more information about the new pre-designed panels and how to request custom designs for them, read the Pre-designed Xenium Prime Gene Expression Panels page and the Getting started guide.
Chemistry version (Xenium v1 or Xenium Prime) is tracked for all custom panel designs
Updated the Advanced target list on the "Tell us about your panel" page to be more comprehensive. Added "SNVs" to the list. As before, select all that apply for your design request.
Added three new human kidney reference datasets
Reduced design build time by optimizing performance
Updated output JSON filename to improve readability and decrease text length
Updated advanced custom domain file CSV outputs for simplicity
Fixed bugs showing wrong panel type selections for pre-existing design IDs

Added support for design of add-on panels for the newly released Human Immuno-Oncology Profiling Panel
Added support for CLOUPE format reference files in addition to H5 and MEX matrices
Enabled accepting and rejecting recommendations when modifying the gene list and probe set counts while iterating on a Xenium custom panel design

Improved probe set coverage for many human and mouse genes, reducing the likelihood that a gene has fewer than eight probe sets available when being included in a Xenium custom design. Read more about our gene coverage in our Getting Started guide.
Improved communication regarding the impact of finalizing a panel design when you enter a design ID that was given to you by a 10x Genomics sales representative.
Added support for .tar.gz reference datasets.

Building a design has been sped up significantly by improving the performance of our probe screening algorithm. This will resolve issues where some users encountered timeouts when designing 480-plex panels with large reference datasets.
When cleaning up your gene list, the Xenium Panel Designer now differentiates between genes that have been removed because we cannot find a match in the Ensembl reference and genes that have been removed because we have zero probes available.
The design summary file now uses reference 'nicknames' rather than reference filenames in the dropdown selectors.
Fixed a bug where reference files that were compressed on macOS led to design errors.

If you are inputting a request for an advanced design, you are now given the option to provide your RNA binding sequences CSV file via the Xenium Panel Designer application (CSV format described in the Technical Note).
When modifying your gene list after a design is generated, the Xenium Panel Designer now displays the reason that we recommend modifying your gene list at the top of the page.
Fixed a bug where you could not navigate back to previous page if the panel designer encountered a timeout when designing your panel.
Fixed a bug where the total number of genes displayed on the panel review page did not update based on your selected finalization choice.

Provide BED files for each panel design iteration.
Introduce limit of 500 MB for uploaded reference datasets in order to improve reliability of the designer. The Xenium Panel Designer computes a pseudobulk matrix from the reference and only requires that all cell types of interest are well represented. Our testing indicates that the end result of 50,000 cell and 1 million cell reference matrices will be very similar.

Enable design of non-advanced human and mouse panels with an existing design ID.
Additional public single cell reference datasets from CELLxGENE are available in the Xenium Panel Designer. We have updated existing reference datasets to ensure all selected single cell references are consistently processed and of high quality.

Add support for design of up to 480-plex standalone custom panels.
Add support for design of add-on panels for the newly released human skin and human colon base panels.

Enable design of human and mouse add-on and standalone custom panels (up to 300 targets) without involvement of 10x Genomics Support team.

Initial release of the Xenium Panel designer, enabling input of design requests for Xenium Custom Panels by providing a gene list and reference single cell transcriptomics datasets.