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Version 0.5.1 `February 10, 2022` | ||
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.. role:: small | ||
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Version 0.5.1 :small:`February 10, 2022` | ||
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- 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>`_] | ||
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Version 0.5.0 `January 24, 2022` | ||
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Version 0.5.0 :small:`January 24, 2022` | ||
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- Add support on 10x Visium spatial data | ||
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- Read the data folder by ``read_input`` function with ``file_type="visium"`` option. | ||
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- Write 10x Visium data to Zarr format by ``write_output`` function with output file name of ``.zarr.zip`` extension. | ||
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Version 0.4.1 `November 4, 2021` | ||
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Version 0.4.1 :small:`November 4, 2021` | ||
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- Fix issues on ``UnimodalData`` object construction. | ||
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Version 0.4.0 `October 19, 2021` | ||
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Version 0.4.0 :small:`October 19, 2021` | ||
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- 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. | ||
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Version 0.3.1 `July 16, 2021` | ||
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Version 0.3.1 :small:`July 16, 2021` | ||
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- 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. | ||
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Version 0.3.0 `July 6, 2021` | ||
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Version 0.3.0 :small:`July 6, 2021` | ||
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- Add support for composite list (e.g. ``[0, pd.DataFrame, np.ndarray]``) in ``data.uns`` field for Zarr read/write. | ||
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Version 0.2.14 `June 28, 2021` | ||
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Version 0.2.14 :small:`June 28, 2021` | ||
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- Add parameter ``uns_white_list`` in ``filter_data`` function to keep QC statistics if needed. | ||
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Version 0.2.13 `June 24, 2021` | ||
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Version 0.2.13 :small:`June 24, 2021` | ||
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- 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. | ||
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Version 0.2.12 `May 28, 2021` | ||
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Version 0.2.12 :small:`May 28, 2021` | ||
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- Bug fix. | ||
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Version 0.2.11 `May 17, 2021` | ||
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Version 0.2.11 :small:`May 17, 2021` | ||
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- Bug fix. | ||
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Version 0.2.10 `February 2, 2021` | ||
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Version 0.2.10 :small:`February 2, 2021` | ||
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- Feature enhancement. | ||
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Version 0.2.9 `December 25, 2020` | ||
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Version 0.2.9 :small:`December 25, 2020` | ||
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- Fix a bug for caching percent mito rate. | ||
- Improve `write_mtx` function. | ||
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Version 0.2.8 `December 7, 2020` | ||
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Version 0.2.8 :small:`December 7, 2020` | ||
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- 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. | ||
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Version 0.2.7 `October 13, 2020` | ||
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Version 0.2.7 :small:`October 13, 2020` | ||
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- Add support for Nanostring GeoMx data format. | ||
- Fix bugs. | ||
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Version 0.2.6 `September 28, 2020` | ||
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Version 0.2.6 :small:`September 28, 2020` | ||
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Fix bug in SCP compatible output generation. | ||
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Version 0.2.5 `August 19, 2020` | ||
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Version 0.2.5 :small:`August 19, 2020` | ||
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Adjustment for Pegasus command usage. | ||
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Version 0.2.2 `June 16th, 2020` | ||
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Version 0.2.2 :small:`June 16th, 2020` | ||
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Fix bugs in data aggregation. | ||
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Version 0.2.1 `June 8th, 2020` | ||
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Version 0.2.1 :small:`June 8th, 2020` | ||
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Fix bug in processing single ``h5`` file. | ||
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Version 0.2.0 `June 7th, 2020` | ||
-------------------------------- | ||
Version 0.2.0 :small:`June 7th, 2020` | ||
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Initial release. |