Cellxgene-census

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1.5.0

R package `cellxgene.census` V1 is out

The Census team is pleased to announce the release of the R package `cellxgene.census`.

This has been long coming since our Python release back in May. Now, from R, computational biologists can access the Census data which is the largest standardized aggregation of single-cell data, composed of >30M cells and >60K genes.

With `cellxgene.census` in a few seconds users can access any slice of Census data using cell or gene filters across hundreds of datasets. The data can be fetched in an iterative fashion for bigger-than-memory slices of data, or quickly exported to basic R structures, and `Seurat` or `SingleCellExperiment` for downstream analysis.

Make sure to checkout the R docs from our doc-site, links can be found in the [github repo chanzuckerberg/cellxgene-census](https://github.com/chanzuckerberg/cellxgene-census/tree/main).

Additions
* [builder] add normalization layer and computed axes statistics by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/612
* [builder] add dataset_version_id by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/618
* [builder] implement worker count limit by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/673
* [python] PCA demo notebook by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/580
* [r] Add `get_single_cell_experiment` by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/640


Fixes
* [docs] cell guide button beta tag alignment by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/657
* [builder] fix merge error in schema doc by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/662
* [docs] Add mean_variance notebook symlink by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/677
* [docs] Fix number of unique cells for human in doc site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/678
* [r] restore vignettes to docsite (in static HTML form) by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/583
* [r] Fix copying R docs, doc-site CI by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/681

What's Changed

* [builder] bump Census build minimum disk space requirement to 1.8TiB by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/661
* [python] bound pytorch memory usage by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/654
* [docs] Fetch docsite version number from git tags by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/675
* [docs] fetch-depth: 0 for docsite build by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/679
* [r] Audit r vignettes by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/686
* [r] Update R docs and doc-site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/684
* [r] run R tests with both release and latest versions of tiledbsoma by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/691
* [r] Change R Dependencies by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/693
* [r] Update DESCRIPTION to remove windows support from R by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/692
* Suggesting very minor edits to comp_bio_data_integration.Rmd by eddelbuettel in https://github.com/chanzuckerberg/cellxgene-census/pull/694
* [r] Update to version 1.5.0 and rebuild doc-site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/695

New Contributors
* eddelbuettel made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/694

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.4.0...v1.5.0

1.4.0

Additions
* Experimental module for calculating out-of-core mean and variance

Fixes/Changes
* Documentation changes to reflect the new LTS release 2023-07-25

What's Changed
* Bump aiohttp from 3.8.4 to 3.8.5 in /tools/cellxgene_census_builder by dependabot in https://github.com/chanzuckerberg/cellxgene-census/pull/632
* fix: dialog by tihuan in https://github.com/chanzuckerberg/cellxgene-census/pull/633
* Expose out-of-core Mean and Variance APIs by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/609
* add a dataset blocklist by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/636
* dataset blocklist location check by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/637
* feat(newsletterBanner): Add localStorage by tihuan in https://github.com/chanzuckerberg/cellxgene-census/pull/643
* Switch to prod role for the builder GHA job by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/644
* [r] hotfix for release directory JSON parsing problem by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/649
* Update builder to use schema_version param to pin dataset CxG schema versions to 3.0.0 by nayib-jose-gloria in https://github.com/chanzuckerberg/cellxgene-census/pull/650
* Updates docs and test results for LTS data release 2023-07-25 by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/652
* Notebooks for LTS 2023-07-25 by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/656
* docs: add cell guide button by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/655

New Contributors
* dependabot made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/632
* nayib-jose-gloria made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/650

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.3.1...v1.4.0

1.3.1

Fixes/changes:
* Documentation and docsite improvements
* Fix issue 622, inconsistent default `census_version` used in various API endpoints

What's Changed
* pin builder dependencies by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/594
* pytorch eager fetch follow-up by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/592
* Adds sparse iter reference docs to doc-site by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/597
* docs: Add newsletter banner by tihuan in https://github.com/chanzuckerberg/cellxgene-census/pull/605
* change error handling for /curation REST errors by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/608
* Add R acceptance tests, update Python acceptance tests by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/576
* Expand doc-site section "Census data releases" and add data erratum by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/600
* [r] get_seurat: allow selection of Seurat `counts` or `data` slot by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/607
* fixes minor documentation issues by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/619
* Complete docstrings for PyTorch ExperimentDataPipe API by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/613
* consistently set default census version to stable by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/623
* add missing census_version param by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/624
* hard error if the builder receives an unsupported CXG schema version by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/625
* add do_not_delete flag to release.json format by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/628

New Contributors
* tihuan made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/605

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.3.0...v1.3.1

1.3.0

Breaking changes

* Remove Python 3.7 support

Additions

* New sparse iterator added to experimental package (591)

Fixes / changes

* Pytorch loader performance improvements and bug fixes
* Update dependency pins for multiple packages
* Documentation updates

What's Changed
* fix incorrect pytorch obs soma_joinids by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/555
* Fix MacOS failing tests by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/557
* remove pytorch_lr_classifier.py by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/556
* Fix doc-site link in README.md by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/571
* Correct pytorch notebook header by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/570
* Avoid unnecessary re-initialization of ExperimentDataPipe in mp mode by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/566
* census cell dup check by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/569
* require s3fs>=2021.06.1 where cache_regions kwarg is added by RemyLau in https://github.com/chanzuckerberg/cellxgene-census/pull/572
* Notebook reformatting by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/579
* [r] install tiledbsoma from github by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/589
* Remove python 3.7 support by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/582
* use less mem for hvg tests by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/590
* Add eager fetching of SOMA batches to ExperimentDataPipe by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/575
* add sparse iterator to experimental.utils by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/591

New Contributors
* RemyLau made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/572

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.2.1...v1.3.0

1.2.1

Additions
* Python 3.11 support
* add notebooks to demonstrate new experimental APIs

Fixes
* Pytorch loader multi-process issues [522, 516]
* Doc site improvements

What's Changed
* fix: pytorch unit test hangs by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/522
* Add support for Python 3.11 by martinkim0 in https://github.com/chanzuckerberg/cellxgene-census/pull/528
* update notebook guidelines by pablo-gar in https://github.com/chanzuckerberg/cellxgene-census/pull/534
* Add docs for experimental modules by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/537
* demo notebook for HVG experimental API by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/536
* Add experimental notebooks to docsite + fix headers by ebezzi in https://github.com/chanzuckerberg/cellxgene-census/pull/541
* fix OOM on pytorch unit test by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/542
* Add pytorch notebook by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/551

New Contributors
* martinkim0 made their first contribution in https://github.com/chanzuckerberg/cellxgene-census/pull/528

**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.2.0...v1.2.1

1.2.0

Add experimental API `cellxgene_census.experimental.pp.get_highly_variable_genes`

What's Changed
* minor clarifications for the pypi.org release process by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/512
* [r] cache most R dependencies to speed up r-check CI by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/517
* [r] Add comp_bio_census_info.Rmd by mlin in https://github.com/chanzuckerberg/cellxgene-census/pull/407
* fix pytorch multiprocessing result by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/516
* Update release_process.md by atolopko-czi in https://github.com/chanzuckerberg/cellxgene-census/pull/520
* highly variable gene annotation by bkmartinjr in https://github.com/chanzuckerberg/cellxgene-census/pull/511


**Full Changelog**: https://github.com/chanzuckerberg/cellxgene-census/compare/v1.1.0...v1.2.0

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