Changes in version 0.2.2                        

Updated on February 23, 2025

Changes to the package include:

  - function get_vectors():
    
      - Input x can also be a named list now. This approach enables
        users to directly input transcript detection coordinates using a
        dataframe. This helps prevent integer overflow issues that may
        arise when creating the SpatialExperiment object for a large
        dataset
    
      - If invalid cluster/sample names are detected, the function
        make.names() will be employed to generate valid names. A message
        will also be displayed to indicate this change.

  - function create_genesets():
    
      - Input x can also be a named list now as in get_vectors()

                        Changes in version 0.2.1                        

Updated on January 20, 2025

Changes to the package include:

  - New Accessors for the Correlation Approach Results:
    
      - Add the function get_cor()
      - Add the function get_perm_p()
      - Add the function get_perm_adjp()

  - New Accessors for Results from the Linear Modeling Approach:
    
      - Add the function get_top_mg()
      - Add the function get_full_mg()

                        Changes in version 0.2.0                        

Updated on November 16, 2024

To enhance interoperability with Bioconductor, the jazzPanda package has
been updated to depend on the following data classes:
SingleCellExperiment, SpatialExperiment, or SpatialFeatureExperiment.

Changes to the package include:

  - Removed Function:
    
      - The convert_data() function has been removed from the export
        list.

  - function get_vectors():
    
      - Input trans_lst is renamed to x.
      - Input cm_lst is removed.
      - x must be a SingleCellExperiment, SpatialExperiment, or
        SpatialFeatureExperiment object.
      - Renamed all_genes to test_genes to store genes for building
        spatial vectors.

  - function compute_permp():
    
      - Input data is renamed to x.
      - n.cores is renamed to n_cores.
      - x must be a SingleCellExperiment, SpatialExperiment, or
        SpatialFeatureExperiment object.

  - function create_genesets():
    
      - Input data_lst is renamed to x.
      - x must be a SingleCellExperiment, SpatialExperiment, or
        SpatialFeatureExperiment object.

                        Changes in version 0.1.1                        

Updated on November 12, 2024

  - Add the convert_data() function to expand interoperability with
    Bioconductor. Support input objects from
    SingleCellExperiment/SpatialExperimentSpatialFeatureExperiment class
  - Modify one input type for function get_vectors(). Renamed input
    parameter data_lst as trans_lst specifically for storing transcript
    coordinates only.

                        Changes in version 0.0.2                        

  - Remove the get_data() function from the package.
  - The get_data() function has been renamed as get_xenium_data() and
    can be used as a help function from vignette.

  - Add a parallel option for the get_vectors() function.

                        Changes in version 0.0.1                        

  - This package is renamed as jazzPanda

  - First version of the spaceMarker package contains functions to
    detect marker genes for image-based spatial transcriptomics data.