NEWS

---

clusterProfiler 4.19.8

• fix: map non-ENTREZID universe in enrichGO (2026-04-22, Wed)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 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

clusterProfiler 4.19.1

• bug fixed in enrichPC (2025-11-01, Sat, #789)

clusterProfiler 4.18.0

• Bioconductor RELEASE_3_22 (2025-10-30, Thu)

clusterProfiler 4.16.0

• Bioconductor RELEASE_3_21 (2025-04-17, Thu)

clusterProfiler 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)

clusterProfiler 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

clusterProfiler 4.14.0

• Bioconductor RELEASE_3_20 (2024-10-30, Wed)

clusterProfiler 4.13.4

• re-export DOSE::enrichDO() and DOSE::gseDO() (2024-10-01, Tue)

clusterProfiler 4.13.3

• fixed bug in enrichPC() (2024-08-26, Mon)

clusterProfiler 4.13.2

• fixed bug of gson_KEGG() (2024-08-19, Mon)

clusterProfiler 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)

clusterProfiler 4.12.0

• Bioconductor RELEASE_3_19 (2024-05-15, Wed)

clusterProfiler 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)

clusterProfiler 4.10.0

• Bioconductor RELEASE_3_18 (2023-10-25, Wed)

clusterProfiler 4.9.5

• fixed R check (2023-10-18, Wed)

clusterProfiler 4.9.4

• use check_installed() to check package dependency (2023-09-08, Fri, #621)
• use yread() in WikiPathway utilities (2023-09-07, Thu)

clusterProfiler 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)

clusterProfiler 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

clusterProfiler 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)

clusterProfiler 4.8.0

• Bioconductor RELEASE_3_17 (2023-05-03, Wed)

clusterProfiler 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)

clusterProfiler 4.7.1

• update according to the KEGG api changes (2023-03-01, Wed)

clusterProfiler 4.6.0

• Bioconductor 3.16 release

clusterProfiler 4.5.3

• GSEA() supports GSONList object (2022-09-21, Wed)
• enricher() supports GSONList object (2022-09-06, Tue)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 4.4.0

• Bioconductor 3.15 release

clusterProfiler 4.3.4

• fix enrichGO , gseGO and groupGO when keyType = 'SYMBOL' && readable=TRUE(2022-4-9, Sat)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 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)

clusterProfiler 4.2.0

• Bioconductor 3.14 release

clusterProfiler 4.1.4

• import yulab.utils (2021-08-20, Fri)

clusterProfiler 4.1.3

• Remove Human Gut Microbiome dataset as the functionalities are provided in https://github.com/YuLab-SMU/MicrobiomeProfiler (2021-08-15, Sun)

clusterProfiler 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)

clusterProfiler 4.1.1

• add citation (new paper published on The Innovation) (2021-07-04, Sun)

clusterProfiler 4.0.0

• Bioconductor 3.13 release

clusterProfiler 3.99.1

• Add new data set, DE_GSE8057, which contains DE genes obtained from GSE8057 (2020-03-08, Mon)

clusterProfiler 3.99.0

• Add KEGG enrichment analysis of Human Gut Microbiome data (2021-02-20, Sat)

clusterProfiler 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)

clusterProfiler 3.18.0

• Bioconductor 3.12 release (2020-10-28, Wed)

clusterProfiler 3.17.5

• update [[.compareClusterResult (2020-10-14, Wed)

clusterProfiler 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

clusterProfiler 3.17.2

• use libcurl if capable (2020-09-08, Tue)
  • https://github.com/YuLab-SMU/clusterProfiler/pull/290

clusterProfiler 3.17.1

• bug fixed of extract_params (2020-08-18, Tue)
  • https://github.com/YuLab-SMU/clusterProfiler/issues/282

clusterProfiler 3.16.0

• Bioconductor 3.11 release

clusterProfiler 3.15.3

• incorporate clusterProfiler.dplyr (2020-03-12, Thu)
  • arrange, filter, group_by, mutate, rename, select, slice and summarize

clusterProfiler 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 :)

clusterProfiler 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.

clusterProfiler 3.14.0

• Bioconductor 3.10 release

clusterProfiler 3.12.0

• Bioconductor 3.9 release

clusterProfiler 3.11.1

• asis parameter in [.compareClusterResult (2018-12-24, Mon)
  • https://github.com/GuangchuangYu/enrichplot/issues/17

clusterProfiler 3.10.0

• Bioconductor 3.8 release

clusterProfiler 3.9.2

• re-export DOSE::gsfilter and DOSE::setReadable (2018-05-25, Fri)

clusterProfiler 3.9.1

• change color scheme of dotplot of compareClusterResult back to red->purple (2018-05-17, Thu)
  • https://support.bioconductor.org/p/108996/

clusterProfiler 3.8.0

• Bioconductor 3.7 release

clusterProfiler 3.7.1

• uniprot_get function (2018-01-30, Tue)
• import enrichplot (2018-01-29, Mon)