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correct css format
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yihming committed Mar 13, 2022
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3 changes: 3 additions & 0 deletions docs/_static/css/my_theme.css
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.small {
font-size:60%;
}
26 changes: 0 additions & 26 deletions docs/_static/my_theme.css

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78 changes: 40 additions & 38 deletions docs/release_notes.rst
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Version 0.5.1 `February 10, 2022`
----------------------------------
.. role:: small

Version 0.5.1 :small:`February 10, 2022`
------------------------------------------

- Make PegasusIO work with Zarr v2.11.0.
- Bug fix in quality control. [PR `#89 <https://github.com/klarman-cell-observatory/pegasusio/pull/89>`_ by `hoondy <https://github.com/hoondy>`_]

Version 0.5.0 `January 24, 2022`
----------------------------------
Version 0.5.0 :small:`January 24, 2022`
-----------------------------------------

- Add support on 10x Visium spatial data

- Read the data folder by ``read_input`` function with ``file_type="visium"`` option.

- Write 10x Visium data to Zarr format by ``write_output`` function with output file name of ``.zarr.zip`` extension.

Version 0.4.1 `November 4, 2021`
----------------------------------
Version 0.4.1 :small:`November 4, 2021`
----------------------------------------

- Fix issues on ``UnimodalData`` object construction.

Version 0.4.0 `October 19, 2021`
---------------------------------
Version 0.4.0 :small:`October 19, 2021`
-----------------------------------------

- Add ``obsp`` and ``varp`` fields to store graph representation in terms of square matrices.
- Allow copy from View of ``AnnData``.
- In ``MultimodalData``, add ``register_attr`` function to register an attribute of a specified type in ``obs`` or ``obsm`` fields. This can be useful for adding information like gene signatures, etc.

Version 0.3.1 `July 16, 2021`
-------------------------------
Version 0.3.1 :small:`July 16, 2021`
--------------------------------------

- For ``aggregate_matrices`` function, allow sample-specific filtration on minimum number of UMIs (``nUMI`` column in sample sheet) and minimum number of genes (``nGene`` column in sample sheet), which would overwrite the corresponding parameters of the function for these samples.

Version 0.3.0 `July 6, 2021`
-------------------------------
Version 0.3.0 :small:`July 6, 2021`
-------------------------------------

- Add support for composite list (e.g. ``[0, pd.DataFrame, np.ndarray]``) in ``data.uns`` field for Zarr read/write.

Version 0.2.14 `June 28, 2021`
-------------------------------
Version 0.2.14 :small:`June 28, 2021`
---------------------------------------

- Add parameter ``uns_white_list`` in ``filter_data`` function to keep QC statistics if needed.

Version 0.2.13 `June 24, 2021`
-------------------------------
Version 0.2.13 :small:`June 24, 2021`
---------------------------------------

- The ``aggregate_matrices`` function now accepts sample sheet in Python dictionary format besides a CSV file path string. See details in its description in API panel.

Version 0.2.12 `May 28, 2021`
-------------------------------
Version 0.2.12 :small:`May 28, 2021`
---------------------------------------

- Bug fix.

Version 0.2.11 `May 17, 2021`
-------------------------------
Version 0.2.11 :small:`May 17, 2021`
--------------------------------------

- Bug fix.

Version 0.2.10 `February 2, 2021`
----------------------------------
Version 0.2.10 :small:`February 2, 2021`
-------------------------------------------

- Feature enhancement.

Version 0.2.9 `December 25, 2020`
-----------------------------------
Version 0.2.9 :small:`December 25, 2020`
------------------------------------------

- Fix a bug for caching percent mito rate.
- Improve `write_mtx` function.

Version 0.2.8 `December 7, 2020`
-----------------------------------
Version 0.2.8 :small:`December 7, 2020`
-----------------------------------------

- Add support on loading ``loom`` file with Seurat-style cell barcode and feature key names.
- Bug fix: resolve an issue on count matrix dimension inconsistency with feature metadata on data aggregation, when last feature has ``0`` count across all cell barcodes. Thanks to `Mikhail Alperovich <misha.alperovich1@gmail.com>`_ for reporting this issue.
- Other bug fix and performance improvements.

Version 0.2.7 `October 13, 2020`
-----------------------------------
Version 0.2.7 :small:`October 13, 2020`
-----------------------------------------

- Add support for Nanostring GeoMx data format.
- Fix bugs.

Version 0.2.6 `September 28, 2020`
-----------------------------------
Version 0.2.6 :small:`September 28, 2020`
-------------------------------------------

Fix bug in SCP compatible output generation.

Version 0.2.5 `August 19, 2020`
--------------------------------
Version 0.2.5 :small:`August 19, 2020`
----------------------------------------
Adjustment for Pegasus command usage.

Version 0.2.2 `June 16th, 2020`
--------------------------------
Version 0.2.2 :small:`June 16th, 2020`
----------------------------------------
Fix bugs in data aggregation.

Version 0.2.1 `June 8th, 2020`
--------------------------------
Version 0.2.1 :small:`June 8th, 2020`
---------------------------------------
Fix bug in processing single ``h5`` file.

Version 0.2.0 `June 7th, 2020`
--------------------------------
Version 0.2.0 :small:`June 7th, 2020`
---------------------------------------
Initial release.

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