PegasusIO for reading / writing single-cell genomics data

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PegasusIO is the IO package for Pegasus.

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Version 0.4.1 November 4, 2021

  • Fix issues on UnimodalData object construction.

Version 0.4.0 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

  • 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

  • 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

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

Version 0.2.13 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

  • Bug fix.

Version 0.2.11 May 17, 2021

  • Bug fix.

Version 0.2.10 February 2, 2021

  • Feature enhancement.

Version 0.2.9 December 25, 2020

  • Fix a bug for caching percent mito rate.

  • Improve write_mtx function.

Version 0.2.8 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 for reporting this issue.

  • Other bug fix and performance improvements.

Version 0.2.7 October 13, 2020

  • Add support for Nanostring GeoMx data format.

  • Fix bugs.

Version 0.2.6 September 28, 2020

Fix bug in SCP compatible output generation.

Version 0.2.5 August 19, 2020

Adjustment for Pegasus command usage.

Version 0.2.2 June 16th, 2020

Fix bugs in data aggregation.

Version 0.2.1 June 8th, 2020

Fix bug in processing single h5 file.

Version 0.2.0 June 7th, 2020

Initial release.