NEWS

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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)