Recent Releases of cellxgene
cellxgene - Release 1.3.0
What's Changed
- Update frontend and backend dependencies
- Added support for python 3.10, 3.11 and 3.12
- Dropped support for python 3.8 and 3.9
Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/v1.2.0...1.3.0
- JavaScript
Published by kaloster almost 2 years ago
cellxgene - Release 1.2.0
What's Changed
- Update frontend and backend dependencies
- Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/1.1.2...v1.2.0
- JavaScript
Published by atarashansky over 2 years ago
cellxgene - Release 1.1.2
What's Changed
- docs: fix test pypi install command by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2515
- feat: Add PR Linting by @seve in https://github.com/chanzuckerberg/cellxgene/pull/2560
- Update license copyright year by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2600
- fix #2608: pin flask requirement to be less than 2.3 by @atarashansky in https://github.com/chanzuckerberg/cellxgene/pull/2609
- chore: Release version 1.1.2 by @atarashansky in https://github.com/chanzuckerberg/cellxgene/pull/2611
Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/1.1.1...1.1.2
- JavaScript
Published by atarashansky about 3 years ago
cellxgene - Release 1.1.1
What's Changed
- chore: fix unit tests by @atarashansky in https://github.com/chanzuckerberg/cellxgene/pull/2562
- docs: updating readme and display version for rebranding by @ashin-czi in https://github.com/chanzuckerberg/cellxgene/pull/2550
- chore: updating Annotate favicon and logo icon by @ashin-czi in https://github.com/chanzuckerberg/cellxgene/pull/2556
- feat: annotate command improvements by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2568
- fix: fix static file serving in webpack by @seve in https://github.com/chanzuckerberg/cellxgene/pull/2574
New Contributors
- @atarashansky made their first contribution in https://github.com/chanzuckerberg/cellxgene/pull/2562
- @ashin-czi made their first contribution in https://github.com/chanzuckerberg/cellxgene/pull/2550
Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/1.1.0...1.1.1
- JavaScript
Published by atolopko-czi over 3 years ago
cellxgene - Release 1.1.0
What's Changed
- add cloud storage support for annotations by @bkmartinjr in https://github.com/chanzuckerberg/cellxgene/pull/2512
- fix: remove unnecessary postgres req by @MDunitz in https://github.com/chanzuckerberg/cellxgene/pull/2524
- chore: replace optimize-css-assets-webpack-plugin with css-minimizer-webpack-plugin by @roaga in https://github.com/chanzuckerberg/cellxgene/pull/2525
- chore(webpack): remove script-ext-html-webpack-plugin by @seve in https://github.com/chanzuckerberg/cellxgene/pull/2534
- chore: skip failing tests to unblock adding of new features by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2545
- fix embedding selection by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2543
- fix: s3 user annotations by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2541
- fix: update actions/setup-python version by @roaga in https://github.com/chanzuckerberg/cellxgene/pull/2528
- use fsspec.download for S3 artifacts + additional logging by @ebezzi in https://github.com/chanzuckerberg/cellxgene/pull/2536
- feat: add cli annotation subcommand by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2539
- fix test by @atolopko-czi in https://github.com/chanzuckerberg/cellxgene/pull/2549
New Contributors
- @roaga made their first contribution in https://github.com/chanzuckerberg/cellxgene/pull/2525
Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/1.0.1...v1.1.0
- JavaScript
Published by seve almost 4 years ago
cellxgene - Release 1.0.1
What's Changed
Bug Fix
- Fix float16 support [#2379] by @blrnw3 in https://github.com/chanzuckerberg/cellxgene/pull/2483 ### Minor Changes
- Update license to 2022. by @maniarathi in https://github.com/chanzuckerberg/cellxgene/pull/2478
- chore(deps): bump follow-redirects from 1.14.2 to 1.14.8 in /client by @dependabot in https://github.com/chanzuckerberg/cellxgene/pull/2484
- chore(deps): bump simple-get from 3.1.0 to 3.1.1 in /client by @dependabot in https://github.com/chanzuckerberg/cellxgene/pull/2489
- chore(deps): bump tmpl from 1.0.4 to 1.0.5 in /client by @dependabot in https://github.com/chanzuckerberg/cellxgene/pull/2490
- chore(deps): bump axios from 0.21.1 to 0.21.4 in /client by @dependabot in https://github.com/chanzuckerberg/cellxgene/pull/2491
- chore(deps): bump nanoid from 3.1.25 to 3.3.1 in /client by @dependabot in https://github.com/chanzuckerberg/cellxgene/pull/2488
- release version 1.0.1 by @seve in https://github.com/chanzuckerberg/cellxgene/pull/2497
Full Changelog: https://github.com/chanzuckerberg/cellxgene/compare/1.0.0...1.0.1
- JavaScript
Published by seve over 4 years ago
cellxgene - Release 1.0.0
Desktop 1.0 Release Notes
- Updated links to documentation
- Fixed a bug with label interactions
- Assorted maintenance
- JavaScript
Published by seve over 4 years ago
cellxgene - Release 0.19.0
New features * Python 3.9 support * The latest gene added appears at the top of the list of genes in Quick Gene Search * Updated front end package dependencies * Assorted maintenance
Bug fixes * Fixed a bug when renaming gene sets
- JavaScript
Published by blrnw3 over 4 years ago
cellxgene - Release 0.18.0
New features - Introduced CLI parameter --X-approximate-distribution for users to specify the distribution of their data, and override the default heuristic determination - For categories with the number of labels over the number set by --max-category-items (default 1000), we now include a label that aggregates all labels over the limit instead of truncating the list of labels
Breaking changes - Removed support for experimental features (--experimental-annotations-ontology, --experimental-annotations-ontology-obo and --experimental-enable-reembedding)
Bug fixes - Fixed a bug in differential expression calculation by changing the t-test calculation to consistently assume normally distributed data, and to log data when data is not normally distributed based on a heuristic - Fixed a bug in --max-category-items
- JavaScript
Published by seve almost 5 years ago
cellxgene - Release 0.17.0
This release contains a new major feature: gene sets! A gene set is a list of genes. You will now be able to visualize the mean expression of a gene set and create and edit gene sets from the UI. Check out our user guide under docs for more information and how to get started.
We’ve also improved differential expression functionality. Now when you run differential expression, 2 lists will be created: one list of 50 highly expressed genes in group 1 and one list of 50 highly expressed genes in group 2.
Please note we will be deprecating Safari support with this release. Please use Chrome, Edge, or Firefox for the best experience.
- JavaScript
Published by signechambers1 almost 5 years ago
cellxgene - Release 0.16.8
Summary: There were two packages that had major updates that caused incompatibility issues with cellxgene: flatbuffers and Flask. In this release, we have pinned both packages to be below the latest 2.0 versions to avoid these incompatibilities (issue #2197).
- JavaScript
Published by maniarathi about 5 years ago
cellxgene - Release 0.16.7
Summary: This release contains bug fixes for a few issues with mismatched colors between the left sidebar and the main canvas (issues #2007 and #2011), and improved error handling for —experimental-annotations-ontology (issue #2024).
- JavaScript
Published by maniarathi over 5 years ago
cellxgene - Release 0.16.6
Summary: We fixed an issue caused by a h5py major version change. As a result, h5py is now restricted to < 3.0.0
- JavaScript
Published by seve over 5 years ago
cellxgene - Release 0.16.5
Summary: We fixed an issue where some of the continuous attributes of cell data were not visible in the right hand side bar as well as an issue with experimental re-embeddings failing.
- JavaScript
Published by maniarathi over 5 years ago
cellxgene - Release 0.16.4
Summary: We fix an issue with colors in the left sidebar not matching the colors in the main canvas area. The Docker contained was updated following a breaking change. We updated the way that static assets are served such that cellxgene can be used behind a proxy. We also corrected an issue with re-embeddings that was broken was small gene counts.
- JavaScript
Published by maniarathi almost 6 years ago
cellxgene - Release 0.16.2
Summary: 0.16.2 corrects a couple of breaking changes from 0.16.0. We fix the bug with gene expression scatterplots where the x and y axes were swapped and we also fix the support of launching cellxgene with the --experimental-enable-reembedding flag.
- JavaScript
Published by maniarathi almost 6 years ago
cellxgene - Release 0.16.0
Summary: 0.16.0 introduced a number of refinements to the cellxgene application. We have added a number of UI enhancements such as histogram coloring, improvements to the differential expression user experience, and re-embeddings. This release also includes a large number of bug fixes and small performance improvements.
We are currently testing an alpha version of a hosted cellxgene at cellxgene.cziscience.com. While it is not yet feature complete, any feedback would be welcome.
Added - Support for coloring right-side histograms #1218 - Config file that provides the ability to set various parameters of launching cellxgene via either the server or the launch CLI command. #1264 - Tooltip for category names #1278 - Compression of HTTP responses for servers launched via the CLI #1285 - Differential expression UI and config visibility improvements #1336 - Support for user-defined category-label colors #1402 - Added ability to select labels for differential expression instead of only subsets #1494 - Improvement to lasso “can close” visual feedback #1550 - Categorial UI improvements including support for renaming the annotations file #1649, #1660 - Support for re-embedding #1679 - experimental. Functionality may change in the future.
Changed - Show single value instead of entire histogram if the minimum and the maximum are the same #1554 - Major refactor to use lazy data loading from the server side using react-async #1571
Fixed
- Added a workaround to accommodate a bug in AnnData make_index_unique that does not work under certain conditions. #1260
- Assorted small UI fixes: proper truncation #1320
- Various histogram fixes like x-axis labeling #1363, performance improvement #1390
- Fix for brushing subset of a gene distribution after subsetting data #1409
- Fix to cache crossfilter when embedding type is changed #1493
- De-duping gene sets #1490
Security
- Removed client package that introduced security vulnerabilities #1248
- JavaScript
Published by maniarathi almost 6 years ago
cellxgene - Release 0.15.0
Summary: 0.15 resolves incompatibilities with the current anndata/scanpy releases, improves ontology-driven label input in user annotations, moves annotations to a supported feature, and resolves a number of miscellaneous bugs and UI issues.
Added:
User annotations feature has moved to a fully supported feature, and is no longer experimental (nb. command line params have changed, and annotations are enabled by default - see documentation for more information).
Experimental support for ontology-driven annotation/label input was further enhanced. Users can now pick from an ontology or define their own label in a single dialog, and ontologies are available for both label and category creation and editing.
Code coverage reports added to the github repo CI pipeline
Significant additions to unit & smoke tests and configuration testing in the CI pipeline
Added experimental support computed re-embedding on user-selected cell sets.
Better handling of annotations with very large number of categorical values.
Changed:
Resolved incompatibility with annata 0.7 and remove pinned Python dependencies for anndata, h5py and tables modules. This resolves several compatibility issues with H5AD files. #1157, #1202
Reset UI replaced with Subset and Unsubset (#1183), and unsubset no longer deletes genes in the right side bar (fixes #1171).
Work in preparation for a web-hosted cellxgene (not yet available or complete), including:
- Incremental loading of data on the front end
- Refactoring the back-end to support a cloud-native data format built upon tiledb.
- #1140, #1163, #1200
Javascript and Python package dependencies updated.
Variety of small UI improvements throughout the application, including more readable data labels on the main graph (#1141, #1160), better handling of long strings (#1206), improved enable/disable state on buttons, etc.
Fixed:
Datasets with more than 32 annotations would occasionally cause the crossfilter to get confused, and selection state to be lost (#1162)
Undo/redo was not working correctly with color-by-annotation and other UI actions (#1165)
- JavaScript
Published by seve over 6 years ago
cellxgene - Release 0.14.1
Fixed: * #1137 - labels do not correctly pan/zoom
- JavaScript
Published by bkmartinjr over 6 years ago
cellxgene - Release 0.14.0
Summary: 0.14.0 adds ontology-based autosuggestions to the experimental annotation feature, category labeling in the main graph/embedding, and a number of bug fixes and incremental improvements.
Added:
* The experimental annotations feature is augmented with the ability to autosuggest labels from an ontology. Ontology is specified from an .obo file. See the --experimental-annotations-ontology command line flag.
* Main embedding (graph) display enhanced with the ability to display category names over the center of the constituent cells. Enabled/disabled by a new UI button in the button bar.
* When launched, cellxgene will inform users when a new version is available on PyPi.org. This check may be bypassed with the new --no-upgrade-check command line option.
Changed:
* Labels / names in the user interface will now display in a sorted order, including embedding names, annotation names, and categorical annotation values.
* Various internal build updates and improvements.
* Fonts needed by the application are now served by the internal web server, rather than relying on internet connectivity.
* Javascript and Python package dependencies updated.
* FAQ link removed from Info menu
* All large histograms will now have a consistent number of bins (PR #1086)
* User-created annotations may now contain additional characters (now allow alphanumeric, plus -_.() and single spaces. Fixes issue #1113.
* The recent 0.7.* release of the anndata module is incompatible with cellxgene. This release pins the anndata dependency to 0.6.22post1 (the most recent compatible version).
Fixed:
* A significant number of bug fixes to experimental annotations, including #1050, #1057, #1036, #1055 and others.
* Annotation file name, specified by --experimental-annotations-file, will now allow file names containing a hyphen. Fixes issue #1072
* Fixed bug which would cause user-created annotations to lose the (mandatory) unassigned category. Fixes issue #1090
* Various layout and whitespace improvements throughout the app.
* Added missing python requests package to requirements.
* Fixed bug that would crash if the user created an annotation name which was the same as another existing annotation name. Fixes issue #1112
* Ensure that all user-created annotation labels are correctly saved, without transformation, to the annotations CSV file. There were several labels (eg, 'nan') which would not be saved correctly to the annotations CSV file. Fixes issue #1111.
* Some sequences of actions caused the undo button to behave unpredictably. This is fixed by #1099
- JavaScript
Published by seve over 6 years ago
cellxgene - Release 0.13.0
Summary: 0.13.0 introduces a layout change, moving all continuous data histograms into a dedicated panel: the "right side bar". In addition, 0.13.0 includes significant improvements and bug fixes to the experimental "user annotation" feature.
Added:
* Introduced a "right side bar" containing all continuous metadata and gene expression histograms.
* [Experimental feature, may be incomplete or unstable] Significant improvements to the user annotation functionality, allowing users to annotate groups of cells with categorical metadata:
* Command line options related to annotation renamed and reorganized -- see cellxgene launch --help for usage.
* Added simple multi-user support for hosted instances of cellxgene, to avoid the possibility of users over-writing each others’ metadata.
* Add a provenance header to the annotations output CSV file.
* Many bug fixes, usability and stability improvements.
Changed:
* Command line option --skip-qc/--run-qc (a toggle) changed to a flag named --skip-qc.
* Command line help (via the --help option) improved.
* Reorganized and improved cellxgene documentation, available at https://chanzuckerberg.github.io/cellxgene/.
* Javascript and Python package dependencies updated.
* Dockerfile now contains python-requests package (#1019).
* Migrate from deprecated Pandas API (#1021).
Fixed: * Various layout issues resolved throughout app.
- JavaScript
Published by bkmartinjr over 6 years ago
cellxgene - Release 0.12.0
Summary: this release adds three major features, in addition to a number of bug fixes and other features:
* The location of the H5AD file may be specified as a URL, in addition to the currently supported file path
* Anndata "backed" mode is supported via --backed command line option
* A new experimental feature: the ability to create new categorical metadata for cells, aka cell annotations.
Added
* cellxgene launch command now accepts a URL as well as file paths. Example: "cellxgene launch http://…" Supports HTTP, HTTPS, and with optional package installations, S3 and GS URLs. (#920)
* New command line option, --backed, will load H5AD file in "backed" mode. This uses less memory, and loads faster. However, it will dramatically increase the time required to load expression histograms or compute differential expression. This feature is most useful to explore metadata and embeddings for very large datasets, or to load only the embedding and metadata on computers with limited memory. This mode is diabled by default.
* New command line option, --about, provides a means to link out to more information about the dataset. The link provided on the command line will appear in the application info menu, and as a link in the dataset title (upper left, next to logo) (#907)
* New command line option, --disable-diffexp, will cause on-demand differential expression (top N gene finding) to be disabled in the application. This is useful when exploring very large datasets, where the differential expression calculation is likely to be extremely slow or unusable due to memory exhaustion. Differential expression is enabled by default.
* Hovering the cursor over a category name will highlight cells in the gene expression scatterplot (previously only highlighted cells in the embedding graph). (#900)
* [Experimental feature, may be incomplete or unstable] Added capability to label cells with new metadata (categorical annotations). This feature is enabled with the "--experimental-label-file" command line option, which requires a CSV file name. User-created metadata will be saved to this file. We would love feedback on this feature - please submit via GitHub issues.
Changed
* Pip install for prepare sub-command is now separate from default installation. If you wish to use prepare, install via pip install cellxgene[prepare]. See getting started guide for more info. (#887, #889)
* Improved layout when strings are long. Will now break/truncate data set title, category name, etc. (#858, #909)
* Improved the formatting for histogram axis labels, better handling of large numbers (#913)
* Significant improvements to the embedding and gene expression plots, including reduction in CPU usage, zoom/pan constraints, a new rendering method designed to highlight meaningful data and improve overall usability/visibility (#893)
* Miscellaneous improvements to documentation and README (#878, #857, #880)
* Python and Javascript package updates, for both security and performance
* Rename "layout" to "embedding" in the UI (#921)
Fixed * Category-specific mini histograms were computed incorrectly in some cases (#869) * Remove pinned matplotlib version, and resolve incompatibility by installing scanpy earlier in the dependency list (so it specifies the matplotlib dependency). * H5py dependency pinned to 2.9.0 to temporarily work around regression reading older anndata files (scanpy issue #832). This will be removed in a future release. (#916). * Fixed several bugs in gene adding (both in bulk and autosuggest). Improved performance for datasets with a very large number of continuous metadata fields.
- JavaScript
Published by bkmartinjr over 6 years ago
cellxgene - Release 0.11.2
Fixed * FIx matplotlib incompatibility error(#877)
- JavaScript
Published by seve almost 7 years ago
cellxgene - Release 0.11.0
Summary
This release implements a requested cellxgene feature: histograms on categorical values vis a vis continuous (see: #762, #616). Color by any continuous variable, like a gene, and see the breakdown of distributions by opening any categorical menu item. This answers questions such as “which clusters expressed which gene?” “What was the breakdown of total gene counts by tissue?” among others.
Added
Added mini histograms to categorical selection, displaying continuous metadata distribution (#827) Added prepare example, updated demo dataset (#810, #803, #547, #529) Documentation regarding hosted instances (#807) Hover on label increases point size of associated cells in graph (#809 #833)
Changed
Updated roadmap (#825) Menu bar code cleanup, logo (#804)
Fixed
Fixed broken URL in docs (#801, #802) Fixed jest tests by removing async (#805)
- JavaScript
Published by colinmegill almost 7 years ago
cellxgene - Release 0.10.1
Changed * Pinned python requirement 'tables==3.5.1' to work around installation failure in recently release of tables 3.5.2
Fixed * Improved main graph scaling and centering of embedding (#784)
- JavaScript
Published by bkmartinjr about 7 years ago
cellxgene - Release 0.10.0
Added * Switch between multiple embedding visualizations in the UI (eg, tsne, umap, etc). (#776, #766) * To add guardrails around very large datasets, CLI will generate a warning if a large sparse non-CSC dataset loaded. (#723) * If a specific port is chosen on the CLI (--port), the app will use it and fail if not able to do so. If no port is specified, the application will scan for an unused port number (#698, #761) * Add logo to UI (#782)
Changed
* Python anndata version dependency updated to >= 0.6.20, resolving the incompatibility with the most recent SciPy release (see anndata issue #146 for details). Also removed the temporary work-around on scipy version requirements introduced in 0.9.3.
* Updated most javascript package dependencies (#765)
* Use anndata to read h5ad files in launch, rather than the ScanPy API wrapper around AnnData. Improves startup speed. (#763)
* Layout of embedding visualization improved. All points will display upon load, and scaling behavior is improved when the window size changes. (#655, #768, #776, #789)
* Pan/zoom scaling is now 1:1 (#722)
* Various testing & CI framework improvements (#777, #772, #757)
* CLI --debug option will generate an error if used with --port option. If you just want verbose error logging, try --verbose.
Fixed
* Fixed several bugs relating to categorical metadata with large (>100) number of categories. (#764, #781, #721, #737)
* Undo/redo bug fix (#787)
* Correctly handle datasets which use a column name "name" in var or obs metadata. (#785)
- JavaScript
Published by bkmartinjr about 7 years ago
cellxgene - Release 0.9.3
Fixed
* Fixed ImportError: cannot import name 'IndexMixin' by excluding conflicting scipy version (#770)
- JavaScript
Published by csweaver about 7 years ago
cellxgene - Release 0.9.2
Fixed * Correctly handle column slicing of csr data (#754)
- JavaScript
Published by csweaver about 7 years ago
cellxgene - Release 0.9.1
Fixed * init.py file missing from new module (#748)
- JavaScript
Published by bkmartinjr about 7 years ago
cellxgene - Release 0.9.0
Added * “Clip” to percentile range for continuous data - (metadata and expression) outside of range will be excluded from histograms and grayed out on layout. This improves handling of zero-heavy distributions, or other cases where outliers need to be suppressed (#570, #672) * Prepare calculates and adds QC metrics as to continuous metadata (uses new ScanPy 'calculateqcmetrics') (#697)
Changed * Documentation updates (#691, #706, #649, #702) * Color-by buttons toggle if clicked twice (#693) * ScanPy requirements updated to 1.3.7(#688) * Server-side refactoring in prep for PyQt & notebook support (#711) * Performance improvements accessing large sparse expression data (#719)
Fixed * Undo/redo improvements - histogram and graph selection now correctly interacts with undo/redo (#679, #663) * Selection of continuous data dimensions containing NaN values would select incorrect cells (#715) * Graph pan/zoom and selection now stay in sync (#622) * Graph selection paints correctly when window resized (#203) * Gene name type-ahead no longer clears text on blur (#573) * Would fail if simplejson was installed in python environment (#700)
- JavaScript
Published by bkmartinjr about 7 years ago
cellxgene - Release 0.8.0
Added * Python 3.7 support * Redo/Undo * (@falexwolf) Support additional graph layouts * Menu with FAQ, etc
Changed * When selected embedding has more than two components cellxgene UI truncates to the first two instead of failing
Fixed * Various UI bug fixes * Histograms no longer allow tiny/invisible selections
- JavaScript
Published by csweaver about 7 years ago
cellxgene - Release 0.7.0
This is largely a performance and refactoring release, with a few small bug fixes.
Changes: * Performance improvements throughout application, due to introduction of a new internal data model and other refactoring (#588, #590, #611) * #610 fixed - Reset slow for large datasets * #617 fixed - negative scalar annotation and expression values were incorrectly displayed
- JavaScript
Published by bkmartinjr over 7 years ago
cellxgene - Release 0.6.1
Fixed * Failed pypi upload due to previously deleted version
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.6.0
Added * Lasso selection tool * Add list of genes
Fixed * (@ivirshup) Serving cellxgene through reverse proxy * Does not error if Content-Type header also include charset * De-duped -d CLI option alias for launch: kept the alias for --diffexp, removed from --debug
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.5.1
Fixed * ModuleNotFoundError: No module named 'server.app.util.fbs'
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.5.0
Added * Performance improvements facilitated by switching to binary (using flatbuffers) for data transport * Scatterplot any two genes * Async busy indicators on slow operations * Non-finite values displayed as gray on graph when coloring by a field and elided from histograms Fixed * Can now run cellxgene container on remote host * Disable cell set buttons until differential expression is cleared Removed * CLI param --nan-to-num removed (non-finite values can be serialized after switching to binary transport)
- JavaScript
Published by csweaver over 7 years ago
cellxgene - 0.4.0
Changes * Add cluster occupancy - when coloring by categorical metadata, stacked barchart shows proportional breakdown of other categorical fields. E.g. color by gender, evaluate gender makeup of each cluster * Add Docker support
- JavaScript
Published by colinmegill over 7 years ago
cellxgene - Release 0.3.0
Changes:
- Add a typeahead, with fuzzy string search, on the Selected Gene text box
- Improve error handling and detection of ScanPy data containing NaN or Infinite values.
- Add --nan-to-num command line parameter to convert NaN/Infinite to finite floating point values.
- Minor improvements to startup speed
Breaking changes:
- Added --host command line option, replacing --listen-all. The equivalent of --listen-all can now be accomplished with --host 0.0.0.0
- JavaScript
Published by bkmartinjr over 7 years ago
cellxgene - Release 0.2.4
Changes
- Update to latest version of sklearn
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.2.3
Changes * Allow downcasting of float64 to float32
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.2.2
Changes * Fixes images on pypi
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.2.1
Fixes issue #457
Changes * Improved handling of numerical and boolean data types
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.2.0
This is the first ‘user ready’ release of cellxgene
Major changes * Launch from CLI with scanpy backend using local data * View and explore cells using a specified dimensionality reduction layout, and show categorical and continuous cell metadata * Explore cells based on their gene expression * Compute differential expression of arbitrary groups of cells * Preprocess data for cellxgene consumption using ‘prepare’ CLI command
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.0.4
Test release-- includes requirements.txt
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Release 0.0.3
Fixes some pip install errors
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Test Release
This is a test release.
- JavaScript
Published by csweaver over 7 years ago
cellxgene - Responsive & performant
This release implements:
- a new layout, with responsive graph and metadata sidebar
- render done in WebGL now instead of canvas
- many performance tweaks by @bkmartinjr
- JavaScript
Published by colinmegill about 8 years ago