To do
- Dependency Review: Considering the removal of the
GEOquery package, as it may no longer be necessary for
preparing GEO series data.
- Plot Customization: All
plot*
functions will be enhanced to allow greater user customization.
- 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.