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clusterProfiler 4.21.1.003

  • align GSEA significance filtering with the historical behavior of clusterProfiler <= 4.18.x: pvalueCutoff now requires both the raw p-value and the adjusted p-value to pass the cutoff, so significant-pathway counts from GSEA()/gseGO()/gseKEGG()/gseMKEGG() are again comparable with the DOSE/fgsea backend (2026-08-14, Thu)
  • restore the seed argument on GSEA(), gseGO(), gseMKEGG() and gseKEGG() and forward it to enrichit::gsea_gson(), so permutation-based GSEA results can be reproduced with a fixed seed (or set.seed() before the call); the argument had been dropped when the enrichit engine was introduced (2026-08-14, Thu)
  • fix get_data_from_KEGG_db() to strip species suffix from pathway names when use_internal_data=TRUE, matching the online path behaviour (2026-08-04, Tue, #783)
  • fix enrichGO() to check whether the OrgDb supports ENTREZID before attempting the ENTREZID-remapping optimisation; custom OrgDb packages without ENTREZID keytype (e.g., non-model organisms) now fall back to the original get_GO_data path instead of throwing an error (2026-08-04, Tue, #823)

clusterProfiler 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)

clusterProfiler 4.20.0

  • Bioconductor RELEASE_3_23 (2026-04-29, Wed)

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

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

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)

clusterProfiler 3.17.1

  • bug fixed of extract_params (2020-08-18, Tue)

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

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

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)