Added local_offset_distance_with_background_fast function which uses dbscan for faster neighour finding.
denoist() now defaults to fast neighbour finding via the neighbour_mode option.
Fixed minor bug where background offset cannot be calculated because an entire gene gets filtered out because of low qv. This should not change existing usage as the issue only arises in extremely small toy datasets.
n_inits can now be tuned in the denoist() function for speed.
Removed print from README.
Fixed minor bug where background offset cannot be calculated because an entire gene gets filtered out because of low qv.
n_inits can now be tuned in the denoist() function for speed.
Removed commented out chunks during development.
Added verbose option to make progress messages off by default.
Replaced dplyr, tidyr, and tibble dependency with base R xtabs.
Specified functions imported from flexmix instead of importing the whole package.
Updated vignette to use BiocStyle.
Trimmed README content for a more pleasant reading experience.
Vignette now uses an even smaller dataset.
local_offset_distance_with_background can now handle non-Xenium transcript
data with no QV column without data modification from user.