To do

1. Dependency Review: Considering the removal of the GEOquery package, as it may no longer be necessary for preparing GEO series data.
2. Plot Customization: All plot* functions will be enhanced to allow greater user customization.
3. New S3 Class: Development of a new S3 class, similar to dgeList, which will offer improved customization and performance.

Version 1.2.3 Changes

• dont run Seurat::DotPlot in vignette to avoid upstream upgrade’s affects

Version 1.2.2 Changes

• fix vignette name in package startup message

Version 1.2.1 Changes

• make each function do a simple task instead of integrating all to a function(check_marker, plotSeuratDot).
• support using custom dataset to annotate and allow user to set the threshold(matchCellMarker2).
• use more convenient input in finsert.
• guess user’s typo input (get_marker).
• update docs and hints.
• set the minimal data.table version to 1.15.0
• support generating plots for each cell type in plotSeuratDot.

Version 1.1.1 Changes

• support argument tissueType and tissueClass in single cell related function.
• fix some typo errors in example-single-cell.R
• update some miscellaneous functions.

Version 1.1.0 Changes

Enhancements

• Artist Class: Now includes a default data argument for data exploration. All commands and results are saved, allowing users to revisit previous analyses.
• Bulk RNA-seq Vignettes: Updated for better usability.
• get_marker() Updates: Added extra messages when searching for undefined cells in the database, improving clarity for users.

Bug Fixes

• prepare_geo() Fix: Non-character ID columns in GPL data are now converted to character to prevent misinterpretation of numeric IDs. Expression data can now be read directly from supplementary files without needing to download them locally.
• plotORA() Fix: Fixed an issue where the plot would fail to display a legend when mapping a variable to the fill aesthetic.

Version 1.0.1 Changes

• NEWS.md File: Added to document changes and updates.
• macOS Compatibility: Fixed an error in uniprot_id_map() on the latest macOS during example usage.
• Vignette Optimization: Vignettes have been updated and optimized for improved performance and usability.