10x Genomics
Single Cell Gene Expression
Cell Ranger, printed on 11/05/2024
Changelog for Loupe Cell Browser 3.1.x (Spring/Summer 2019)
Improvements in 3.1.1
General Improvements
- Fixes Split View bugs when importing custom projections.
- Fixes default name of screenshot export.
- Correctly update filter UI elements after switching between filters.
Gene Expression Improvements
- Support antibody-only datasets.
- Render UMAP projections computed by the Cell Ranger 3.1 pipeline.
- Bugfix: fix UMI Count overcount on datasets generated with Cell Ranger 3.0.
- Share heatmap filtering options with the data table.
- Add ability to drive the differential expression heatmap with a feature list.
- Correctly size the differential expression heatmap when the bottom panel is
resized.
- Fix case where selecting Total UMI Count for multi-species datasets could
trigger a crash.
ATAC Improvements
- Speeds up display of motif z-scores.
- Fixes case where fragments file may be incorrectly reported as not pertaining
to a dataset.
- Avoids hanging when opening a file saved with a feature list containing both a
motif and nearby gene.
New Features in 3.1.0
Filtering
Filter for cell types by creating complex boolean filters. For example, to
filter for mature B Cells, you could create the statement
(CD79A OR CD79B) AND TCL1A = 0. Please refer to the
filtering section in the tutorial
for further guidance on how to use this feature.
Projection Import
Import data from your favorite projection methods using a simple CSV format. For
more details on the file format, please check the
projections section of the interoperability documentation
Multi-Windows
You can now have multiple windows open simultaneously. This will allow you to
compare aspects of the same dataset side by side or keep concurrent analyses
open at one time. To create new windows, you can click on File > New Window
within Loupe Cell Browser or double click on a cloupe file.
Feature Expression Coloring
We've provided a variety of alternate colormaps from which to choose.You can
also manually adjust the endpoints of the colorscale. View the
alternate colorscales and manual ranges
documentation for more details.
Projection Settings
Exports of the barcode plot will now include the relevant legend (categories or
gene/feature expression). Barcode plot point size will now scale with zoom
level. There is also an option to manually increase or decrease the marker size.
To find out more about changing marker size, read the
modifying marker size
documentation.
Updates and Bugfixes
- "Active Feature List" now saves to the cloupe file
- Feature Plot exports with axes labels
- See the full cluster name while hovering in both the categories panel and in
the barcode plot
- Get email address to submit feedback in the help menu
- Default filenames for barcode plot exports includes sample id
- Improved feature list search performance
