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CHANGELOG.md

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Changelog

Unreleased

-   Add ability to search for categories in loom annotations
-   Removed cross-species search functionality for Drosophila datasets

March 3, 2020

  • Version 1.8.2

    • Fix issue getting regulon data in edge case
    • Fix issue with tracebacks not being displayed on the server

  • Version 1.8.1

    • Fix issue with comments not being displayed on annotations
    • Fix issue with expression values being double scaled

February 24, 2020

  • Version 1.8.0
    • Add GDPR compliant cookie warning
    • Implement login with ORCID ID
      • Logging in with an ORCID ID provides access to collaborative annotation functions
    • Implement collaborative annotation for read-write sessions
      • Clusters can now be annotated with controlloed vocabularies (via EBI OLS) or free text.
      • Other users can vote on annotations
      • Once added, annotations can be searched by other users
    • Expand config options and enable use of config.json file to be passed at runtime
    • Decrease page size on marker tables for performance
    • Fix a bug in colors overflowing into other channels
    • Add legend on compare tab
    • Fix color indexing on compare tab
    • Enable legend for 'All Clusters'
    • Improve loading of looms when only one is required
    • Fix issue displaying targets of regulons without all metadata
    • Limit search results for single letter queries
    • Save generated search spaces to disc to improve loading times after server has been restarted
    • Switch to path based store for active connections
      • This propagates changes to a file to all active connections (when triggered)
    • Begin implementation of Python type hints
    • General code cleanup
    • Generate mypy typings on protobuf creation
    • Various other fixes and performance increases (See commit history)

January 24, 2020

  • Version 1.7.3
    • Fix a bug in storing current session

November 12, 2019

  • Version 1.7.2
    • Fix bug Regulon tab not showing for loom files not containing otif-based and track-based regulons.
  • Version 1.7.1
    • Fix display of regulon target gene occurrences with loom containing motif-based and track-based regulons.

November 9, 2019

  • Version 1.7.0
    • Display the regulon target gene occurrences when running SCENIC in multi-runs mode.

October 21, 2019

  • Version 1.6.0
    • Allow renaming of file hierarchy levels from frontend

October 9, 2019

  • Version 1.5.0
    • Add functionality for renaming clusters from the frontend on read-write looms
    • Bump to loompy 3
    • Small read/write bug fixes

October 1, 2019

  • Version 1.4.2
    • Autodetect dimensionality reductions from column attributes with 'pca', 'tsne' or 'umap' in the name. NOTE: Extracts first 2 dimensions from attributes with >=2 dimensions. Therefore 3D dimensions may appear in the list but will show as 2D.

September 28, 2019

  • Version 1.4.1
    • Fix bug in the query results (clusters) when searching a cluster which the queried gene is a marker for.

August 1, 2019

  • Version 1.4.0
    • Enabled searching of regulons via their targetted genes
    • Enabled searching of clusters by their marker genes
      • Loom files containing many clusters will now search slower as a result
    • General search space and search improvements
      • Only build search space once per file on load
        • Initial load times of a session may increase as a result, however time for searcing is halved as a result
      • Reordering of search results
      • Increased number of results returned when searching and enabled scroll bar
    • EXPERIMENTAL: Enabled searching genes linked to regions for scATAC-seq data
      • To enable this, a row attribute must be added called linkedGene containing a string of the gene linked to the region
    • Allow display of Aertslab v9 motifs

July 18, 2019

  • Version 1.3.7
    • Enabled read only sessions on the backend for permanent sessions
      • Use by adding a tab-seperated value of either ro or rw to a session in Permanent_Sessions.txt in SCope config dir.
    • No longer open looms as rw all the time to prevent corruption when closing the server.
    • Converted logs from print statements to logging package.
    • Various small fixes and dependancy issues.
    • General code cleanup and PEP8 compliance changes

June 26, 2019

  • Version 1.3.6
    • Allow for running in dev mode on AWS through npm run scope-dev-aws (useful for t2.micro AWS instance). See here to start your own SCope instance running on AWS. Update related tutorials for AWS deployment.

December 14, 2018

  • Version 1.3.5
    • Update Apache config to deploy SCope on secure protocol (e.g.: HTTPS). Update related tutorials for AWS deployment.

November 16, 2018

  • Version 1.3.4
    • Fix some installation bugs.
    • Fix bug Compare tab disabled when a .loom does not contain any meta data information (e.g.: annotations).

August 22, 2018

  • Version 1.3.2
    • Fix bug downloading sub loom when parent loom is a public one.
    • Fix bug downloading sub loom when parent loom has been created with SCopeLoomR version < 0.0.5.6558.
  • Version 1.3.1
    • Fix bug when cluster markers not present in .loom.
  • Version 1.3.0
    • Add feature to download subset of looms. Currently it is only possible to subset the active loom based on cluster information.

August 10, 2018

  • Version 1.2.1
    • Fix bug when trajectory data not well defined in .loom.

July 6, 2018

  • Version 1.2.0
    • Add feature to display trajectory data in the viewer. Currently the only way we provide to add trajectory data to .loom files is through SCopeLoomR.

July 4, 2018

  • Version 1.1.0
    • Add feature to display metrics in the viewer. Currently the only way we provide to add metrics to .loom files is through SCopeLoomR.