# 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 (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) - # 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 + `asis` parameter in `[.compareClusterResult` (2018-12-24, Mon) - # 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) - # 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)