NEWS

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jazzPanda 1.1.2

Updated on Oct 14, 2025

• Minor bug fix for Bioconductor devel.

jazzPanda 1.1.1

Updated on June 24, 2025

Changes to the package include:

• function get_vectors():

  • Parameters w_x and w_y have been removed. Spatial windows are now automatically determined per sample using a 5% buffer around the coordinate range.
  • Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.

• function create_genesets():

  • Parameters w_x and w_y have been removed. Spatial windows are now computed per sample using a 5% buffer based on input coordinates.
  • Improved handling of genes that are only detected in a subset of samples. If a gene is not present in a sample, a zero-filled vector is used for that sample to maintain consistent vector lengths across samples.

• function compute_permp():

  • Parameters w_x and w_y are no longer required. Spatial boundaries are now automatically derived per sample using a 5% buffer.

jazzPanda 1.0.1

Updated on Sep 1, 2025

Changes to the package include:

• function get_vectors():

  • Buffer used for auto-detecting spatial windows has been changed from 5% to a fixed value of 1e-6.
  • Added a new parameter to allow exporting the calculated bounding box for each sample.

• function compute_permp():

  • Buffer for automatic spatial boundaries is now set to 1e-6.
  • Fixed spatial bin indexing issues to ensure correct alignment when calcualting spatial vectors with count matrix.

• Backported updates from version 1.1.1 on Bioconductor devel

jazzPanda 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()

jazzPanda 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()

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 0.0.2

• 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.

jazzPanda 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.