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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

clusterProfiler 3.17.1

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)