perform_linda_analysis function to handle
multi-group comparisons correctlylog2FoldChange column to the results for
effect size informationAdded Gene Set Enrichment Analysis (GSEA) functionality with the following new functions:
pathway_gsea(): Performs GSEA analysis, supporting
KEGG, MetaCyc, and GO pathwaysvisualize_gsea(): Creates visualizations of GSEA
results, including enrichment plots, dotplots, barplots, network plots,
and heatmapscompare_gsea_daa(): Compares GSEA and Differential
Abundance Analysis (DAA) resultsgsea_pathway_annotation(): Adds pathway annotations to
GSEA resultsggpicrust2_extended(): Provides integrated analysis
combining ggpicrust2 and GSEA functionalityImproved network and heatmap visualization capabilities with richer parameter options and better error handling
Added preliminary support for MetaCyc and GO pathways
Fixed various bugs and optimized code structure
Refactored the package dependencies, moving most Bioconductor packages from Imports to Suggests, reducing mandatory dependencies.
Added conditional checks to ensure that packages are only used when they are available.
Fixed the function export issue, ensuring that all public API functions are correctly exported.
Updated the example code, improving its stability and compatibility.
Updated the documentation format to comply with the latest CRAN standards.
Fixed invalid URL links in the README.
Optimized code quality, removing unused variables.
Added missing import declarations to ensure package integrity.
NEWS.md file to track changes to the
package.