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Cell Ranger


10x Genomics
Single Cell Gene Expression

Changelog for Loupe Cell Browser 3.1.x (Spring/Summer 2019)

Improvements in 3.1.1

General Improvements

Gene Expression Improvements

ATAC Improvements

New Features in 3.1.0


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


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