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jazzPanda 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.

jazzPanda 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.

jazzPanda 0.0.1

  • This package is renamed as jazzPanda

spaceMarker 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.

spaceMarker 0.0.2

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

spaceMarker 0.0.1

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