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()
:
x
can also be a named list now as in get_vectors()
Updated on January 20, 2025
Changes to the package include:
New Accessors for the Correlation Approach Results:
get_cor()
get_perm_p()
get_perm_adjp()
New Accessors for Results from the Linear Modeling Approach:
get_top_mg()
get_full_mg()
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:
convert_data()
function has been removed from the export list.function get_vectors()
:
trans_lst
is renamed to x
.cm_lst
is removed.x
must be a SingleCellExperiment
, SpatialExperiment
,
or SpatialFeatureExperiment
object.all_genes
to test_genes
to store genes
for building spatial vectors.function compute_permp()
:
data
is renamed to x
.n.cores
is renamed to n_cores
.x
must be a SingleCellExperiment
, SpatialExperiment
,
or SpatialFeatureExperiment
object.function create_genesets()
:
data_lst
is renamed to x
.x
must be a SingleCellExperiment
, SpatialExperiment
,
or SpatialFeatureExperiment
object.Updated on November 12, 2024
convert_data()
function to expand interoperability with
Bioconductor. Support input objects from
SingleCellExperiment/SpatialExperimentSpatialFeatureExperiment classget_vectors()
.
Renamed input parameter data_lst
as trans_lst
specifically for storing
transcript coordinates only.get_data()
function from the package.get_data()
function has been renamed as get_xenium_data()
and
can be used as a help function from vignette.get_vectors()
function.