Release Notes

  • 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