Single Cell ATAC
Cell Ranger ATAC, printed on 04/01/2023
What's New in Loupe Browser 5.0
Loupe Browser 5.0 is primarily a release in support of the Single
Cell Gene Expression and Immune Profiling assays, with new support
for online, guided filtering and reclustering of single-cell gene
For more information about filtering and reclustering updates for gene
expression datasets, click here,
or visit the filtering and reclustering page.
Improvements For All Applications
Concurrent Installation with Previous Releases
Loupe Browser 5.0 can be installed concurrently with a currently
installed version of Loupe Browser 4.0 or lower. This is required
to be able to support visualization of VDJ data created by Cell Ranger 4.0
Support for Cell Ranger 5.0 VDJ Datasets
Loupe Browser 5.0 now only supports the loading of VDJ clonotypes created
with Cell Ranger 5.0 and later. Previous versions of Loupe Browser may
be used to look at VDJ data generated by Cell Ranger 4.0 and earlier.
Differential expression is now more intuitively tied to the active
category. If a differential expression calculation has not been
run for the currently selected category, the differential expression
table and heatmap will appear blank and prompt you to run the
calcuation, instead of showing the most recently calculated differential
Changelog for Loupe Browser 5.0.x
Loupe Browser 5.0.1 (February 3, 2021)
- Adds support for pyramid TIFFs, or TIFFs with multiple pages of the same image at different resolutions, in the Visium manual aligner.
- Updates differential expression and violin plots to reflect currently visible data.
- More clearly indicates when differential expression has not yet been calculated for an active category or set of clusters.
- Fixes bug where differential expression fails when viewing data points not in the currently visible projection.
- Fixes bug where reclustering calculation never completes on certain Windows machines.
- Fixes bug when switching between feature plot and other projections.
- Fixes crash when deleting an imported projection in a multiome ATAC + gene expression dataset.
- Adds error message when an imported projection name duplicates an existing projection name (such as "tsne").
- Changes default export name for differential expression table.
- Updates the certificate on the Windows installer.