Changes in version 4.21.1 - support UniProt accession -> KO conversion in bitr_kegg() via KEGG REST and export gson_KO() for KEGG Orthology workflows (2026-06-24, Wed) - add nseGO(), nseKEGG(), nseMKEGG(), nseWP(), mnseGO(), mnseKEGG(), mnseMKEGG(), and mnseWP() as high-level topology-aware enrichment wrappers powered by enrichit, with metadata backfilling and lightweight wrapper tests (2026-06-24, Wed) - re-export aggregate_omics(), aggregate_enrichment(), harmonize_ids(), and select_features_for_ora() from enrichit for high-level multi-omics workflows (2026-06-24, Wed) - get_ppi_network to download and cache the full STRING PPI network for a specific species (2026-06-23, Tue) - the getPPI is now alias to get_ppi - fix GSEA wrappers to restore eps, forward extra arguments such as sampleSize to enrichit::gsea_gson(), and align the GSEA method documentation with the current enrichit interface (2026-06-22, Mon, #822) - re-export bayes_enrich() and bayes_summary() from enrichit (>= 0.1.5) for Bayesian term selection and posterior-ranked summaries of ORA enrichment results (2026-06-16, Tue) Changes in version 4.20.0 - Bioconductor RELEASE_3_23 (2026-04-29, Wed) Changes in version 4.19.8 - fix: map non-ENTREZID universe in enrichGO (2026-04-22, Wed) Changes in version 4.19.7 - interpret(), interpret_agent(), and interpret_hierarchical() now use aisdk's global default model when model = NULL, so users can switch the package-wide default with aisdk::set_model() while still overriding per call with an explicit model argument (2026-03-31, Tue) Changes in version 4.19.6 - update ko2name() to robustly parse KO names via KEGG REST, support vector input with deduplication, and return NA when NAME is missing (2026-02-25, Wed) - bug fixed for plot.interpret (2026-02-05, Thu) Changes in version 4.19.5 - interpret() prompt optimized with 'Comparative Analysis' and 'Rule of Exclusion' to better distinguish cell types with shared functions (e.g. NK vs CD8+ T cells) using specific marker genes (2026-01-22, Thu) - fixed a bug in interpret() where empty interpretation results were returned due to incorrect list structure handling in process_enrichment_input (2026-01-22, Thu) - interpret() now considers specific marker genes in cell type annotation to avoid key markers being overshadowed by general pathways (2026-01-21, Wed) - optimize enrichGO() to avoid memory boom when keyType is not ENTREZID (2026-01-21, Wed, #805) - gson_GO_local() to support local GO annotation by adding ancestral terms (2026-01-21, Wed) - interpret() implements a gene-based fallback mode for clusters with no enriched pathways, ensuring comprehensive analysis (2026-01-20, Tue) - plot() method for interpretation object to visualize the LLM-inferred regulatory network using ggtangle (2026-01-20, Tue) - interpret_agent() supports multi-agent system (Deep Mode) for interpretation (2026-01-20, Tue) - Agent Cleaner: Filters noise and selects relevant pathways - Agent Detective: Identifies key regulators and functional modules using PPI/TF data - Agent Synthesizer: Synthesizes findings into a coherent narrative - interpret() supports 'Knowledge-Guided Interpretation' (2026-01-20, Tue) - add_ppi parameter to integrate PPI network and identify hub genes - gene_fold_change parameter to incorporate expression levels - Mixed-source enrichment analysis support (e.g. Pathways + TFs) for causal integration - LLM-guided network refinement to output core regulatory networks - interpret_hierarchical() for hierarchical interpretation (e.g. Major -> Minor clusters) (2026-01-20, Tue) - interpret() now supports prior parameter for reference-guided interpretation (e.g. from SingleR/scGPT) (2026-01-20, Tue) Changes in version 4.19.4 - interpret() now supports task parameter to specify the task: 'interpretation', 'annotation' and 'phenotyping' (2025-01-18, Sat) - interpret() supports enrichResult, gseaResult, compareClusterResult and list of enrichment results (2025-01-18, Sat) Changes in version 4.19.3 - instead of packing KEGG cache data in the package, we now download it from https://yulab-smu.top/clusterProfiler (2025-12-15, Mon) - add github action to automatically update KEGG cache data (2025-12-09, Tue) - use 'enrichit' as engine for enrichment analysis (2025-12-07, Sun) Changes in version 4.19.2 - use 'quarto' as vignette engine (2025-11-20, Thu) - update KEGG cache data (2025-11-20, Thu, #792) - number of KEGG pathway with category information: 582 - Number of species: 11344 Changes in version 4.19.1 - bug fixed in enrichPC (2025-11-01, Sat, #789) Changes in version 4.18.0 - Bioconductor RELEASE_3_22 (2025-10-30, Thu) Changes in version 4.16.0 - Bioconductor RELEASE_3_21 (2025-04-17, Thu) Changes in version 4.15.2 - more general regular pattern to remove species suffix in KEGG pathway name (2025-02-27, Thu) - remove input duplicated genes in groupGO() (2024-11-29, Fri, #741) Changes in version 4.15.1 - simplify() keeps the most informative term if there exist multiple terms that meets the criteria (2024-11-29, Fri, #744) - add 'RichFactor', 'FoldEnrichment' and 'zScore' in enrichDAVID() result (2024-11-12, Tue) - update DAVID Web Service URL to make enrichDAVID() work properly (2024-11-09, Sat) - https://davidbioinformatics.nih.gov/content.jsp?file=WS.html - add new citation (2024-11-07, Thu) - https://doi.org/10.1016/j.xinn.2024.100722 Changes in version 4.14.0 - Bioconductor RELEASE_3_20 (2024-10-30, Wed) Changes in version 4.13.4 - re-export DOSE::enrichDO() and DOSE::gseDO() (2024-10-01, Tue) Changes in version 4.13.3 - fixed bug in enrichPC() (2024-08-26, Mon) Changes in version 4.13.2 - fixed bug of gson_KEGG() (2024-08-19, Mon) Changes in version 4.13.1 - update functions to access PathwayCommons data (2024-08-11, Sun, gson#9) - use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri) - update kegg_category information (7 categories and 572 subcategories) (2024-07-26, Fri) - Cellular Processes (36) - Drug Development (75) - Environmental Information Processing (41) - Genetic Information Processing (39) - Human Diseases (99) - Metabolism (190) - Organismal Systems (92) Changes in version 4.12.0 - Bioconductor RELEASE_3_19 (2024-05-15, Wed) Changes in version 4.10.1 - bug fixed in parsing KEGG category (2024-03-07, Thu, #664) - update citation (#656) and wikipedia data URL (2024-01-10, Wed, #633) Changes in version 4.10.0 - Bioconductor RELEASE_3_18 (2023-10-25, Wed) Changes in version 4.9.5 - fixed R check (2023-10-18, Wed) Changes in version 4.9.4 - use check_installed() to check package dependency (2023-09-08, Fri, #621) - use yread() in WikiPathway utilities (2023-09-07, Thu) Changes in version 4.9.3 - enrichKEGG() and gseKEGG() now supports organism = 'cpd' to accept KEGG Compound ID (2023-08-31, Thu) - gson_cpd() and gson_ko() - use yulab.utils::yread() to parse file (2023-08-15, Tue) - supports Pathways Common (2023-08-02, Wed, #613) Changes in version 4.9.2 - append_kegg_category() function to add KEGG pathway category information to KEGG enrichment result and now it is the default behavior of enrichKEGG() and gseKEGG() (2023-07-12, Wed) - parse KEGG Pathway Category information (2023-07-11, Tue) - mv parse_gff() to GOSemSim::read.gaf() and re-export (2023-07-10, Mon) - mv buildGOmap() to `GOSemSim::buildGOmap() and re-export Changes in version 4.9.1 - getPPI() to query PPI network from 'stringdb' (2023-05-15, Mon) - getTaxID() and getTaxInfo() functions to query taxonomy information (2023-05-14, Sun) Changes in version 4.8.0 - Bioconductor RELEASE_3_17 (2023-05-03, Wed) Changes in version 4.7.2 - change wikiPathways link. (2023-03-10, Fri) - update get_data_from_KEGG_db() for the KEGG api changes (2023-03-05, Sun) - removing species info at the end of KEGG pathway names (2023-03-05, Sun) Changes in version 4.7.1 - update according to the KEGG api changes (2023-03-01, Wed) Changes in version 4.6.0 - Bioconductor 3.16 release Changes in version 4.5.3 - GSEA() supports GSONList object (2022-09-21, Wed) - enricher() supports GSONList object (2022-09-06, Tue) Changes in version 4.5.2 - support passing a GSON object to enricher(USER_DATA) and GSEA(USER_DATA) (2022-8-01, Mon) - gson_kegg_mapper() allows building a gson object from outputs of KEGG Mapper service (2022-07-29, Fri, #492) - fix show method for compareClusterResult (2022-06-21, Tue, #473) - gson_KEGG() download latest KEGG and output a GSON object (2022-06-08, Wed) - support passing a GSON object to gseKEGG(organism) - support passing a GSON object to enrichKEGG(organism) (2022-06-06, Mon) Changes in version 4.5.1 - follow KEGG api upgrade that change from http to https (2022-06-06, Mon) - use 'wininet' to download KEGG data when .Platform$OS.type = "windows" (2022-06-03, Fri) - mv read.gmt and read.gmt.wp to the 'gson' package and reexport these two functions from 'gson' (2022-04-28, Thu) - fix compareCluster when fun = enrichPathway(2022-4-28, Thu) Changes in version 4.4.0 - Bioconductor 3.15 release Changes in version 4.3.4 - fix enrichGO , gseGO and groupGO when keyType = 'SYMBOL' && readable=TRUE(2022-4-9, Sat) Changes in version 4.3.3 - parse GAF file to prepare GO annotation data (esp for proteomic study) (2022-03-08, Tue, #397, #418, #421, #442) - bug fixed in compareCluster() (2022-01-27, Thu, #424) Changes in version 4.3.2 - bug fixed in extract_params() (2022-01-12, Wed, #392, @amcdavid) - make simplify() works for gseGO() in compareCluster() - support formula interface for GSEA methods in compareCluster() (2022-01-04, Tue, @altairwei, #416) Changes in version 4.3.1 - compareCluster() supports GSEA algorithm (2021-12-11, Sat) - update error message of download.KEGG.Path() and download.KEGG.Module()(2021-11-21, Sun) - update simplify() function to support ont = ALL (2021-10-27, Wed) Changes in version 4.2.0 - Bioconductor 3.14 release Changes in version 4.1.4 - import yulab.utils (2021-08-20, Fri) Changes in version 4.1.3 - Remove Human Gut Microbiome dataset as the functionalities are provided in https://github.com/YuLab-SMU/MicrobiomeProfiler (2021-08-15, Sun) Changes in version 4.1.2 - update citation and DESCRIPTION (2021-08-15, Sun) - update kegg_species.rda and allow online download using KEGG api (2021-08-14, Sat) Changes in version 4.1.1 - add citation (new paper published on The Innovation) (2021-07-04, Sun) Changes in version 4.0.0 - Bioconductor 3.13 release Changes in version 3.99.1 - Add new data set, DE_GSE8057, which contains DE genes obtained from GSE8057 (2020-03-08, Mon) Changes in version 3.99.0 - Add KEGG enrichment analysis of Human Gut Microbiome data (2021-02-20, Sat) Changes in version 3.19.1 - setting default timeout to 300 for downloads (2021-02-05, Fri) - fixed download method setting - capable of setting KEGG download method via options(clusterProfiler.download.method = METHOD) (2020-12-31, Thu) Changes in version 3.18.0 - Bioconductor 3.12 release (2020-10-28, Wed) Changes in version 3.17.5 - update [[.compareClusterResult (2020-10-14, Wed) Changes in version 3.17.3 - internal suports of enrichment analyses using WikiPathways (2020-09-09, Wed) - enrichWP for ORA analysis - gseWP for GSEA analysis - get_wp_organisms for listing supported organisms - read.gmt.wp for parsing gmt file downloaded from wikiPathways Changes in version 3.17.2 - use libcurl if capable (2020-09-08, Tue) - https://github.com/YuLab-SMU/clusterProfiler/pull/290 Changes in version 3.17.1 - bug fixed of extract_params (2020-08-18, Tue) - https://github.com/YuLab-SMU/clusterProfiler/issues/282 Changes in version 3.16.0 - Bioconductor 3.11 release Changes in version 3.15.3 - incorporate clusterProfiler.dplyr (2020-03-12, Thu) - arrange, filter, group_by, mutate, rename, select, slice and summarize Changes in version 3.15.2 - remove Suggests of KEGG.db as it will be deprecated in Bioconductor 3.11 (2020-01-14, Tue) - optimize enrichGO to use less memory (2019-12-13, Fri) - re-implement read.gmt without using GSEABase, and my own version is much more fasta :) Changes in version 3.15.1 - e.g. user can pass fun=enrichGO to compareCluster without quoting enrichGO (2019-12-02, Mon) - add keytype and readable info in compareCluster output - mv compareClusterResult class defintion to DOSE (2019-11-02, Sat) - mv fortify, barplot and dotplot for compareClusterResult to enrichplot. Changes in version 3.14.0 - Bioconductor 3.10 release Changes in version 3.12.0 - Bioconductor 3.9 release Changes in version 3.11.1 - asis parameter in [.compareClusterResult (2018-12-24, Mon) - https://github.com/GuangchuangYu/enrichplot/issues/17 Changes in version 3.10.0 - Bioconductor 3.8 release Changes in version 3.9.2 - re-export DOSE::gsfilter and DOSE::setReadable (2018-05-25, Fri) Changes in version 3.9.1 - change color scheme of dotplot of compareClusterResult back to red->purple (2018-05-17, Thu) - https://support.bioconductor.org/p/108996/ Changes in version 3.8.0 - Bioconductor 3.7 release Changes in version 3.7.1 - uniprot_get function (2018-01-30, Tue) - import enrichplot (2018-01-29, Mon)