NEWS.md

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

ggpicrust2 2.1.1

Bug Fixes

• Improved error handling for KEGG database connections (Issue #138):
• Added robust error handling for HTTP 404 errors when connecting to the KEGG database
• Function now continues processing other KO IDs even when some IDs return HTTP 404 errors
• Added detailed logging about which KO IDs were not found
• Only throws a fatal error when all KO IDs fail to be processed

• Includes summary statistics about successful, not found, and error counts

• Fixed the LinDA analysis for multi-group comparisons (Issue #144):

• Modified the perform_linda_analysis function to handle multi-group comparisons correctly
• The function now creates separate result entries for each pairwise comparison
• Added the log2FoldChange column to the results for effect size information

ggpicrust2 2.1.0

Major Changes

• Added Gene Set Enrichment Analysis (GSEA) functionality with the following new functions:
• pathway_gsea(): Performs GSEA analysis, supporting KEGG, MetaCyc, and GO pathways
• visualize_gsea(): Creates visualizations of GSEA results, including enrichment plots, dotplots, barplots, network plots, and heatmaps
• compare_gsea_daa(): Compares GSEA and Differential Abundance Analysis (DAA) results
• gsea_pathway_annotation(): Adds pathway annotations to GSEA results

• ggpicrust2_extended(): Provides integrated analysis combining ggpicrust2 and GSEA functionality

• Improved 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

ggpicrust2 2.0.1

Major Changes

• Fixed a bug in the pathway_annotation function, resolving issues caused by changes in the KEGG API response structure

ggpicrust2 2.0.0

主要变更

• 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.

ggpicrust2 1.7.5

ggpicrust2 1.7.2

ggpicrust2 1.7.1

ggpicrust2 1.7.0

ggpicrust2 1.6.6

ggpicrust2 1.6.5

ggpicrust2 1.6.4

ggpicrust2 1.6.3

ggpicrust2 1.6.2

ggpicrust2 1.6.1

ggpicrust2 1.6.0

ggpicrust2 1.5.1

ggpicrust2 1.5.0

ggpicrust2 1.4.12

ggpicrust2 1.4.11

ggpicrust2 1.4.10

ggpicrust2 1.4.9

ggpicrust2 1.4.8

ggpicrust2 1.4.7

ggpicrust2 1.4.6

ggpicrust2 1.4.5

ggpicrust2 1.4.4

ggpicrust2 1.4.3

ggpicrust2 1.4.2

ggpicrust2 1.4.1

ggpicrust2 1.4.0

ggpicrust2 1.3.1

ggpicrust2 1.3.0

ggpicrust2 1.2.3

ggpicrust2 1.2.2

ggpicrust2 1.2.1

ggpicrust2 1.2.0

ggpicrust2 1.1.1

ggpicrust2 1.1.0

ggpicrust2 1.0.1

ggpicrust2 1.0.0

ggpicrust2 0.2.0

• Added a NEWS.md file to track changes to the package.

ggpicrust2 documentation built on April 13, 2025, 9:08 a.m.