NEWS

---

clusterProfiler 4.21.3

• fix get_kegg_species() and kegg_taxa() for KEGG's retirement of the organism special database name: https://rest.kegg.jp/list/organism now answers HTTP 400 while the rest of the REST API keeps working, so the weekly "Update KEGG Data" workflow and any user calling search_kegg_organism(use_internal_data = FALSE) failed with "cannot open URL ... HTTP status was '400 Bad Request'". Both now read /list/genome, which returns the same organisms as <T number>\t<code>; <scientific name> (<common name>); the species list is parsed from the name and code of that single column. An organism without a common name keeps its scientific name in common_name, as it did before (2026-10-18, Sun)
• restore_hybrid_result() and restore_entrez_result_ids() map a gene set's IDs back to the source keyType with one vectorized pass instead of one labels[ids] + unname() per set. On a BP result (~5,900 tested sets, 390k ID slots) that loop cost 7.5 s per call and compareCluster() calls it once per cluster; the vectorized form takes 0.2 s and is byte-identical, including list names, empty sets and geneID order (pinned by a test). hybrid_ids_for_input() likewise replaces a per-id mapping$source == id scan with a single split and named lookup (negligible wall time at cluster-sized inputs, but no longer quadratic in the mapping size). Measured on the PBMC 10k 13-cluster SYMBOL compareCluster() together with the enrichit fixes: 140 s -> about 70 s (run-to-run 69-78 s), with 7,489 rows, p-values (difference 0), Counts and geneID sets identical (2026-10-18, Sun)
• enrichGO() caches the hybrid GSON it builds for a non-ENTREZID keyType when some input IDs cannot be mapped to Entrez. Without a universe, that build reads every key of the OrgDb and therefore depends only on (organism, ont, keyType), but compareCluster() calls enrichGO() once per cluster and rebuilt it every time (7.7 s per call on human GO BP, PBMC 10k, 13 clusters, 2026-10-18). The hybrid path itself is unchanged and still fires ONLY when an input ID has no Entrez mapping -- an all-mappable input keeps the existing fast path and never builds hybrid data -- while a universe-scoped or evidence-filtered call neither reads nor writes this cache (2026-10-18, Sun)
• read.gmt.pc() now reads the fields of a Pathway Commons gene set description by their labels rather than by splitting the string at every "; ". A pathway name that holds a semicolon, such as Phospholipase C-mediated cascade; FGFR2, is no longer cut short and its datasource, organism and idtype stay in their own columns; previously the extra pieces were merged into the last field, so the fields were shifted one to the left and nothing said so. A description that declares fewer fields than expected returns NA for the missing one instead of failing the whole read, and enrichPC() and gsePC() take the species from the first gene set that declares an organism (#789, 2026-10-08, Thu)
• fix enrichGO() with a non-ENTREZID keyType when some source IDs cannot be mapped to Entrez: the memory-saving Entrez annotation remains the fast path, while unmapped source IDs are added through direct native-key annotations and analyzed in one hybrid GSON; when universe is omitted, the effective annotated hybrid background is constructed and reported by message instead of silently dropping IDs (#829, 2026-10-03, Sat)
• restore the original source keyType consistently after the Entrez optimization and readable conversion, including result metadata and projected gene-set memberships (#829, 2026-10-03, Sat)

clusterProfiler 4.21.2

• enrichMKEGG() and gseMKEGG() accept a GSON object for organism, as enrichKEGG()/gseKEGG() already did, so KEGG module enrichment can run against a locally built annotation (gson_KEGG()) when KEGG is unreachable; they also now stop with "organism should be a species name or a GSON object" instead of an unrelated error from the organism mapper. The organism documentation for the KEGG functions now mentions the GSON option at all (2026-09-22, Tue, #623)
• enrichGO() takes an evidence argument to restrict the GO annotation by evidence code before the analysis, e.g. evidence = c("IDA", "IPI", "IMP") to keep manually supported annotations or evidence = "IEA" for electronic ones only; dropping IEP is the usual way to avoid circular reasoning when the gene sets come from co-expression clustering. Because the annotation (and hence the background) changes, the result is not simply a subset of the unfiltered run, and filtered runs are not cached (2026-09-22, Tue, #160)
• enrichGO() no longer aborts with missing value where TRUE/FALSE needed when an OrgDb's organism cannot be identified — an AnnotationHub OrgDb, for example. The cached-GO-data check compared the cached organism against get_organism(OrgDb) in a bare if(), and that comparison is NA for such an OrgDb, so the second call in a session failed with an error that named none of this; an unidentifiable organism is now treated as "not cached" and the annotation is rebuilt (2026-09-22, Tue, #232)
• Gff2GeneTable() now reads Ensembl/GTF-style GFF3 as well as NCBI/RefSeq files: it accepts a gene_id= attribute (Ensembl) in addition to GeneID= (NCBI) and takes the gene symbol from Name=/gene_name= when gene= is absent. Previously an Ensembl file left every key NA, and merging two all-NA key columns is a cartesian product — useful-looking but wrong on a small file and negative length vectors are not allowed on a real genome. A file with neither identifier style now stops with a message saying what is expected (2026-09-22, Tue, #193)
• add_go_level() appends a level column giving the GO level of every enriched term (1 = the ontology root), so results can be kept to a band of levels with e.g. subset(res, level >= 3 & level <= 6); the level is taken from the ontology the term itself belongs to, so ont = "ALL" and compareCluster() results are labelled term by term (2026-09-22, Tue, #793)
• simplify() now infers the ontology from the GO IDs when the result object does not carry one, instead of refusing: this covers a gseaResult whose @setType holds a collection name rather than an ontology (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) as well as an enrichResult from enricher(), which previously required assigning x@ontology by hand; results spanning several ontologies are simplified as GOALL, and non-GO gene sets are still rejected with a message that says so (2026-09-22, Tue, #753, #369)
• compareCluster() now warns when a non-character universe is supplied: it wraps each per-cluster call in suppressMessages(), which used to swallow the underlying enrichment function's "universe is not in character and will be ignored" message, so a numeric universe appeared to be accepted while having no effect (2026-09-22, Tue, #654)
• gsePC() and gseWP() now expose an eps argument and forward it to GSEA() (and on to enrichit::gsea_gson()), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG() (2026-09-22, Tue)
• fix gson_cpd() to use the compound KEGG REST endpoint; enrichKEGG(organism = 'cpd') had been failing since KEGG retired /link/cpd/pathway, which now returns HTTP 400 (2026-09-22, Tue, #828)
• kegg_rest() now reports a failed download where it happens, telling an unreachable network apart from an HTTP error status and from an empty response; previously these surfaced much later as an obscure error (2026-09-22, Tue)
• download.KEGG.Path() and download.KEGG.Module() now stop with an actionable message when the downloaded annotation is empty, or when the gene/pathway table shares no ID with the pathway-name table, instead of returning an empty annotation that downstream surfaced as a misleading "No gene can be mapped"; this replaces an is.null() guard that could never fire (2026-09-22, Tue, #146, #378, #561, #646)
• 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

• 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)