Release Notes

  • 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.post3 September 10, 2021
    • Fixed error computing differential expression in cirro prepare_data using Pegasus/Cumulus when categories contain the : character

  • 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.post3 August 13, 2021
    • Compute complete differential expression results in cirro prepare_data using Scanpy or Pegasus/Cumulus

  • 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

  • 1.1.13 February 1, 2021
    • Explore complete differential expression results generated by Scanpy or Pegasus/Cumulus

    • Added reverse option to color schemes

  • 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