What's New in HISE?

Recent Changes

Date	Change
2025-05-14	Released pipeline for Cell Ranger version 9.0.1 for flex RNA runs in HISE. To read the full details, review our documentation and the official 10x Genomics release notes. The previous version of Cell Ranger remains available. To continue using the previous version, keep your submission sheet as is. To update to the new version, specify `frna-v3` in the Type column of the Header tab on your Submission Sheet.
2025-04-29	Revised version of document published: Create, Edit, or Delete Metadata.
2025-04-21	Launched the Xenium pipeline, which enables spatial transcriptomics analysis within HISE, converting raw Xenium data into formats that can be analyzed, explored, and visualized. For details, see Use the Xenium Pipeline (Tutorial).
2025-03-14	Extended the IDE timeout period from 30 min to 12 hr.

In the current release we added the following features:

We support adding cohort, subject, sample, demographics and other metadata for external data, such as reference data sets
As is already the case for assay data processed by automated pipelines, we now support defining and declaring assay data not processed by automated pipelines such that the data can be easily found via advanced search, the data availability dashboard and the sample status dashboard

Enhancing the functionality of what was previously known as project folders, all HISE projects now have a project store, and all analysts have access to the files in the store.
New files destined for a project store can now be ingested along a submission sheet, declaring its associated metadata such as sample reference. Metadata declaration can also be done for already ingested files via the project store page (in your personal space). Metadata declaration ensures your data can be more easily found in advanced search by collaborators
Jupyter Notebooks now have interactive UI to facilitate storing derived data in a HISE project store or permanent store, and reference that data and Jupyter Notebook in a Study. Declaring derived data in this manner enable study collaborators to more easily find your analysis approach and results

The uploadFiles method has been extended to store data either in a permanent or project store. Data sets now need to be given a data type such that derived data can be more easily found in search.
All methods related to project folder have been deprecated and might be removed in a future release. To access project store data, use readFiles/cacheFiles instead (this requires that files have a sample reference).
Isolated files in a project store can still be deleted. Files in a project store can also be moved to the permanent store to prevent accidental deletion.
Methods to change the state of your virtual machine are now available.
- R
  - stopIDE()
- Python
  - stop_ide()

For publications, authors can now add their Orcid ID, affiliation and sources of funding