Release Notes
- 1.1.57 September 29, 2023
Ensure group order is persisted when performing differential expression between two groups
Fixed drop-down arrow click for gene sets
Show delete dataset from open dataset dialog
- 1.1.56 August 25, 2023
Updated display for differential expression between two groups
- 1.1.55 August 16, 2023
Support saving specific fields in prepare_data command
- 1.1.54 April 26, 2023
Read Xenium output
- 1.1.53 April 25, 2023
Added keyboard shortcuts for selecting active chart
- 1.1.52.post2 April 21, 2023
Fixed swapping row and column spot coordinates for Space Ranger output prior to version 2.0
- 1.1.52.post1 April 21, 2023
Fixed error parsing command line argument in concat command
- 1.1.52 April 20, 2023
Added option to invert categorical filters
Added search to categorical legend
Compute and visualize cellular trajectories interactively
Added support for Space Ranger 2.0 output
Added concat command to concatenate spatial and non-spatial embeddings
- 1.1.51 March 22, 2023
Support saving default visualization state in database
- 1.1.50 March 20, 2023
Support saving/loading anndata layers in parquet format
- 1.1.49 March 16, 2023
Fix bug where heatmap custom color range had no effect
- 1.1.48 January 26, 2023
Fix error using gene filter when performing differential expression between two selected groups
- 1.1.47 January 23, 2023
Show last updated date in dataset browser
Improved memory consumption for spatial datasets
- 1.1.46 January 3, 2023
Fix error using lasso selection when performing differential expression between two selected groups
- 1.1.45 December 12, 2022
Added option to download job result without opening
Show renamed category names in composition plot
Show legend in saved composition plot image
Fix error performing differential expression between two selected groups
- 1.1.44 November 21, 2022
Fix bug when multiple gene features fail to update
- 1.1.43 November 8, 2022
Support multiple lasso/box selections for spatial images
- 1.1.42 October 21, 2022
Added range filters for features and continuous metadata fields
- 1.1.41 September 30, 2022
Distribution tab updates: Show selection on top. Toggle visibility of selected and non-selected distributions
Added taxonomy field to new dataset dialog
Added option to save categorical color scheme to file
- 1.1.40 September 23, 2022
Sort clusters by percentage of selected cells within a cluster only updates when button is clicked
Added option to sort clusters by number of selected cells within a cluster
- 1.1.39 September 13, 2022
Fixed sorting clusters by percentage bug
- 1.1.38 September 9, 2022
Fixed authenticating with Google on Safari and FireFox
- 1.1.37 September 8, 2022
Added option to sort clusters by percentage of selected cells within a cluster
- 1.1.36 July 18, 2022
Updated support for Google OAuth 2.0 and App Engine
Ensure anndata layers are stored in sparse csc format in cirro prepare_data
- 1.1.35 July 1, 2022
Fixed error when selecting more than one layer in anndata layers
- 1.1.34 June 22, 2022
Added support for anndata layers
- 1.1.33 June 10, 2022
Fixed error computing differential expression results using scanpy in cirro prepare_data with older h5ad files
Raise error in cirro prepare_data when specified group not found in dataset
- 1.1.32 May 20, 2022
Fix error saving spatial datasets in cirro prepare_data
Updated dot plot tooltips
Added Okta integration
- 1.1.31 May 5, 2022
Fix error when setting a color manually when more than 40 category values
Improved differential expression filter user interface
- 1.1.30 May 5, 2022
Show percent cells in dot plot
- 1.1.29 April 11, 2022
Skip groups with less than 3 cells when computing differential expression results in cirro prepare_data
- 1.1.28 April 4, 2022
Fixed incompatibility with some datasets prepared with an earlier version of cirrocumulus
- 1.1.27 March 30, 2022
Fixed incompatibility with Flask 2.1
- 1.1.26 March 17, 2022
Fixed incompatibility with anndata 0.8.0
Fixed error when normalizing differential expression results
- 1.1.25.post4 March 8, 2022
Minor user interface updates
- 1.1.25.post3 February 25, 2022
Fixed error displaying differential expression results
- 1.1.25.post2 February 23, 2022
Fixed bug in which lower values were sometimes rendered on top of higher values in embedding chart
Performance improvements
- 1.1.25.post1 January 13, 2022
Preserve colors in h5ad file in cirro prepare_data
Set environment variable CIRRO_AUTH_CLIENT_ID to enable OAuth 2.0 with Google
User interface updates
- 1.1.25 December 20, 2021
Added option to compute differential expression results for all groups vs. rest
Updated tooltip display
- 1.1.24.post4 December 2, 2021
Removed –email flag from cirro serve
Fixed error storing large precomputed results
- 1.1.24.post3 November 23, 2021
Enable double-click to select on spatial images
Use spawn for running background jobs
Fixed bug in which dataset dialog remained open on save
Fixed error getting precomputed results
- 1.1.24.post2 November 19, 2021
Fixed error editing dataset
- 1.1.24.post1 November 15, 2021
Fixed error selecting all features in differential expression results
Added additional fields for new datasets
- 1.1.24 November 10, 2021
Changed default output format to zarr in cirro prepare_data
Fixed error retrieving job results stored in GridFS
- 1.1.23.post1 November 9, 2021
Fixed gzip encoding when writing to remote storage (e.g S3)
- 1.1.23 November 3, 2021
Style updates
Fixed error loading differential expression results
- 1.1.22.post10 November 2, 2021
Made left-side drawer collapsible
Fixed error saving cluster markers
Improved point size when saving embedding images
- 1.1.22.post9 October 29, 2021
Fixed error showing gallery labels
- 1.1.22.post8 October 28, 2021
Show zero cells instead of all cells when no cells pass filters
- 1.1.22.post7 October 28, 2021
Fixed default color scale for displaying features in sets
Changed single-click to double-click for selecting categorical values on primary embedding
- 1.1.22.post6 October 25, 2021
Preserve embeddings when multiple datasets passed to cirro prepare_data
Fixed error saving dataset views
- 1.1.22.post5 October 22, 2021
Separate color schemes for continuous observations, features, and modules
Explore gene modules stored in adata.uns[‘module’]
- 1.1.22.post4 October 19, 2021
Added ability to select all members of a set
Fixed bug displaying renamed category labels on embedding
Added option to integrate Mixpanel. Set environment variable CIRRO_MIXPANEL to your project token to track open dataset events
- 1.1.22.post3 October 13, 2021
Fixed bug that required two clicks to load differential expression results
Remove jobs from database when deleting datasets
- 1.1.22.post2 October 12, 2021
Fixed error when computing differential expression between two lasso’ed selections using cirro serve
Fixed display of “Sign In” button using cirro serve
Added ability to control the visibility of table columns in dataset chooser
- 1.1.22.post1 October 8, 2021
Save categorical legend scroll bar position when switching features
- 1.1.22 October 7, 2021
Added –ontology option to cirro serve and cirro launch
Fixed error saving colors from h5ad files in cirro prepare
Added option to search specific fields in dataset chooser
Save results in GridFS when using MongoDB without –results option
- 1.1.21 October 5, 2021
Removed –backed option in cirro launch
Added zarr format support in cirro prepare_data
Added –results option to cirro serve and cirro launch
Added ability to compute differential expression between all pairs of clusters
Select category by clicking cell on an embedding
- 1.1.20.post4 September 17, 2021
Style updates
- 1.1.20.post2 September 9, 2021
cirro prepare_data can output directly to S3 or GCP bucket
- 1.1.20.post1 September 8, 2021
Save categorical colors to database
Save cluster positive and negative markers to database
- 1.1.20 September 2, 2021
Added static website hosting capabilities
Performance improvements
- 1.1.19.post1 August 25, 2021
Fixed error getting precomputed results
- 1.1.19 August 25, 2021
Show distributions for numerical cell metadata
Improve interactive differential expression performance
- 1.1.18 August 16, 2021
cirro prepare_data accepts multiple input datasets to better support multimodal data
- 1.1.17.post4 August 13, 2021
Fixed error in cirro launch that prevented h5ad files from loading
- 1.1.17.post2 August 11, 2021
Preserve category order only when < 1000 categories
Synchronize 3-d gallery chart rotation with primary view
Added separate marker size for filtered points
- 1.1.17.post1 June 29, 2021
Fixed error computing differential expression results when using cirro launch
- 1.1.17 June 28, 2021
Added TileDB support
- 1.1.16.post3 June 3, 2021
Embedding chart performance improvements
Replace saved filters with links in order to save complete state
- 1.1.16.post2 May 26, 2021
Drag and drop chips to reorder
Handle thousands of categories in violin plot
- 1.1.16.post1 April 28, 2021
Plot selected cells on top of unselected cells in embedding chart
- 1.1.16 April 28, 2021
Enable selecting top markers by a field in ascending or descending order
Updated auto-display logic
- 1.1.15.post4 April 22, 2021
Changed –header flag in cirro serve to accept Markdown file
- 1.1.15.post3 April 20, 2021
Fixed opening files with drive names on Windows
- 1.1.15.post2 April 13, 2021
Fixed error adding new dataset on Google App Engine
Show cirrocumulus version
- 1.1.15.post1 April 12, 2021
Moved composition plot to separate tab
Added –header flag to cirro serve to customize application header
Auto-display cluster annotation by default
- 1.1.15 April 6, 2021
Added composition plot
Pass –upload flag to cirro serve to enable file uploads
Show plot tooltips in bottom bar
Export data from dot plot
- 1.1.14.post5 March 30, 2021
Fixed issue that distribution charts did not update when color scheme changed
- 1.1.14.post4 March 26, 2021
Fixed issue that primary embedding chart did not update when color scheme changed
- 1.1.14.post3 March 9, 2021
Added ability to customize footer in cirro serve
- 1.1.14.post2 March 2, 2021
Click and drag to resize primary embedding chart
Added landing page
- 1.1.14.post1 February 24, 2021
Fixed error performing interactive differential expression analysis using cirro launch
Sort gallery charts by first by feature and then by embedding
- 1.1.14 February 23, 2021
Added interactive differential expression analysis
To add to current selection, hold down the Ctrl or Command keys when using lasso or box select tools
- 1.1.13.post2 February 10, 2021
Added standardize option that scales each feature or categorical group from zero to one for distributions and results visualization
Added species to dataset import when using cirro serve
Added option to show/hide labels in embedding gallery
cirro launch now accepts Seurat objects
- 1.1.13.post1 February 2, 2021
Added sort functionality to full differential expression results visualization
- 1.1.12 January 20, 2021
Added violin plots
- 1.1.11.post3 December 14, 2020
Include categorical labels and dot plot options in Copy Link URL
- 1.1.11.post2 December 8, 2020
Use anndata.uns[field_colors] if present for cell metadata default colors
Added ability to view features in saved sets
Use reticulate to convert Seurat objects to h5ad in cirro prepare_data
- 1.1.11.post1 December 6, 2020
Convert seurat_clusters cell metadata field in Seurat objects to categorical in cirro prepare_data
- 1.1.11 December 4, 2020
Automatically compute cluster markers when using cirro prepare_data without –group flag
Show categorical labels on gene/feature embedding plots
Updated code for reading Seurat objects in cirro prepare_data
- 1.1.10.post8 November 24, 2020
Fixed error in cirro prepare_data when saving cell metadata names containing spaces
- 1.1.10.post7 November 23, 2020
Plot higher values on top of lower values for continuous values in saved embedding image.
Improved performance computing markers using cirro prepare_data with –group flag
- 1.1.10.post6 November 20, 2020
Fixed bug that prevented genes in sets from being displayed in selection dot plot.
- 1.1.10.post5 November 18, 2020
Fixed error when computing markers using cirro prepare_data with –group flag
Added ability to enter dataset description in Markdown when using cirro serve
- 1.1.10.post4 November 12, 2020
Toggle between dot plot and heatmap
- 1.1.10.post3 November 6, 2020
Added option to change dot plot color scheme
- 1.1.10.post2 October 30, 2020
Fixed display of set names
Fixed bug updating selected dot plot when selection changes
- 1.1.10.post1 October 28, 2020
Create dot plots by grouping by more than one category
Search dataset names and descriptions when using cirro serve
- 1.1.10 October 25, 2020
Fixed error selecting more than one cell metadata field
- 1.1.9.post3 October 21, 2020
Fixed error on startup using cirro launch
- 1.1.9.post2 October 20, 2020
Fixed serving spatial images using cirro serve
- 1.1.9.post1 October 13, 2020
Fixed error reading old datasets generated with cirro prepare_data
- 1.1.9 October 13, 2020
Added user interface to create gene/feature sets
- 1.1.8.post5 October 5, 2020
Updated dataset chooser
- 1.1.8.post4 October 2, 2020
Added dataset descriptions
- 1.1.8.post3 October 1, 2020
Show labels in gallery
Updated dark mode
- 1.1.8.post2 September 29, 2020
Removed active list. Select a feature/category to view details and filter
- 1.1.8.post1 September 25, 2020
Shuffle plot order in embedding plot for categorical values
Fixed scrolling bug in active list
- 1.1.8 September 24, 2020
Added support for generic spatial data in addition to 10x visium
Made primary embedding chart responsive
Added option to set min and max of color scale
Updated gallery chart size
Updated prepare_data command
Changed dot plot default min to zero
Added option to dot plot mean and percent expressed scales
- 1.1.7.post3 September 18, 2020
Plot higher values on top of lower values in embedding plot
- 1.1.7.post2 September 17, 2020
Save state when toggling between datasets
Fixed bug in dot plot tooltips
Changed dot plot color scheme
- 1.1.7.post1 September 2, 2020
Fixed bug passing markers to launch command
launch command takes multiple datasets
- 1.1.7 August 28, 2020
Use median instead of mean for categorical label position on data
Fixed Safari embedding label shadow bug
Save pan and zoom values in link URL
- 1.1.6 August 27, 2020
Added option to set embedding label font size
Show shadow around embedding label
- 1.1.5.post3 August 26, 2020
Fixed embedding label and tooltip color in dark mode
Fixed embedding label font size
- 1.1.5.post2 August 25, 2020
Save additional chart options when copying link
Support multiple differential expression results produced by Scanpy
- 1.1.5.post1 August 24, 2020
Fixed dot plot background color in dark mode
- 1.1.5 August 24, 2020
Allow dataset sharing within an email domain
Added additional 3-d chart options
Added dark theme
Added timeout to serve command
Support markers generated with Pegasus
- 1.1.4 August 17, 2020
Added spatial support
- 1.1.3 August 13, 2020
Improved support for Google authentication in serve command
- 1.1.2.post2 August 12, 2020
Fixed bug in prepare_data for saving markers
Added gunicorn and pymongo to requirements
- 1.1.2.post1 August 11, 2020
Added pyarrow to requirements
- 1.1.2 August 11, 2020
Show separate dot plots for all cells and selected cells
Added support for renaming clusters
Added prepare_data command for generating cirrocumulus formatted files for viewing on the cloud
Added ‘serve’ command to serve multiple users and datasets
- 1.1.1 July 24, 2020
Load marker genes from h5ad or JSON file
- 1.1.0.post3 July 17, 2020
Fixed embedding hover formatting issue
- 1.1.0.post2 July 16, 2020
Fixed Safari bug that caused gallery images to be flipped
Improved performance loading local h5ad files
- 1.1.0.post1 June 15, 2020
Fixed bug that sometimes prevented dot plot from showing
- 1.1.0 June 1, 2020
Added support for STARFusion output
Include labels in saved image
- 1.0.1 May 7, 2020
Draw labels on embedding
- 1.0.0 May 5, 2020
Lasso and box selection
- 0.0.6.post2 Mar 25, 2020
Added tabs for navigation
Use pandas for serialization
- 0.0.6.post1 Mar 20, 2020
Improved chart performance
- 0.0.6 Mar 19, 2020
Gallery view
- 0.0.5 Mar 19, 2020
Export filters
- 0.0.4 Jan 16, 2020
Autorotate 3d embeddings
- 0.0.3.post2 Jan 14, 2020
Save local filters to file
- 0.0.3.post1 Jan 9, 2020
Support 3d embeddings
- 0.0.3 Jan 9, 2020
Added filters
Added launch command
- 0.0.2 Nov 5, 2019
Initial release