Changes in version 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
Changes in version 4.14.0
- Bioconductor RELEASE_3_20 (2024-10-30, Wed)
Changes in version 4.13.4
- re-export DOSE::enrichDO() and DOSE::gseDO() (2024-10-01, Tue)
Changes in version 4.13.3
- fixed bug in enrichPC() (2024-08-26, Mon)
Changes in version 4.13.2
- fixed bug of gson_KEGG() (2024-08-19, Mon)
Changes in version 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)
Changes in version 4.12.0
- Bioconductor RELEASE_3_19 (2024-05-15, Wed)
Changes in version 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)
Changes in version 4.10.0
- Bioconductor RELEASE_3_18 (2023-10-25, Wed)
Changes in version 4.9.5
- fixed R check (2023-10-18, Wed)
Changes in version 4.9.4
- use check_installed() to check package dependency (2023-09-08, Fri,
#621)
- use yread() in WikiPathway utilities (2023-09-07, Thu)
Changes in version 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)
Changes in version 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
Changes in version 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)
Changes in version 4.8.0
- Bioconductor RELEASE_3_17 (2023-05-03, Wed)
Changes in version 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)
Changes in version 4.7.1
- update according to the KEGG api changes (2023-03-01, Wed)
Changes in version 4.6.0
- Bioconductor 3.16 release
Changes in version 4.5.3
- GSEA() supports GSONList object (2022-09-21, Wed)
- enricher() supports GSONList object (2022-09-06, Tue)
Changes in version 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)
Changes in version 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)
Changes in version 4.4.0
- Bioconductor 3.15 release
Changes in version 4.3.4
- fix enrichGO , gseGO and groupGO when keyType = 'SYMBOL' &&
readable=TRUE(2022-4-9, Sat)
Changes in version 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)
Changes in version 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)
Changes in version 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)
Changes in version 4.2.0
- Bioconductor 3.14 release
Changes in version 4.1.4
- import yulab.utils (2021-08-20, Fri)
Changes in version 4.1.3
- Remove Human Gut Microbiome dataset as the functionalities are
provided in https://github.com/YuLab-SMU/MicrobiomeProfiler
(2021-08-15, Sun)
Changes in version 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)
Changes in version 4.1.1
- add citation (new paper published on The Innovation) (2021-07-04,
Sun)
Changes in version 4.0.0
- Bioconductor 3.13 release
Changes in version 3.99.1
- Add new data set, DE_GSE8057, which contains DE genes obtained from
GSE8057 (2020-03-08, Mon)
Changes in version 3.99.0
- Add KEGG enrichment analysis of Human Gut Microbiome data
(2021-02-20, Sat)
Changes in version 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)
Changes in version 3.18.0
- Bioconductor 3.12 release (2020-10-28, Wed)
Changes in version 3.17.5
- update [[.compareClusterResult (2020-10-14, Wed)
Changes in version 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
Changes in version 3.17.2
- use libcurl if capable (2020-09-08, Tue)
- https://github.com/YuLab-SMU/clusterProfiler/pull/290
Changes in version 3.17.1
- bug fixed of extract_params (2020-08-18, Tue)
- https://github.com/YuLab-SMU/clusterProfiler/issues/282
Changes in version 3.16.0
- Bioconductor 3.11 release
Changes in version 3.15.3
- incorporate clusterProfiler.dplyr (2020-03-12, Thu)
- arrange, filter, group_by, mutate, rename, select, slice and
summarize
Changes in version 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 :)
Changes in version 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.
Changes in version 3.14.0
- Bioconductor 3.10 release
Changes in version 3.12.0
- Bioconductor 3.9 release
Changes in version 3.11.1
- asis parameter in [.compareClusterResult (2018-12-24, Mon)
- https://github.com/GuangchuangYu/enrichplot/issues/17
Changes in version 3.10.0
- Bioconductor 3.8 release
Changes in version 3.9.2
- re-export DOSE::gsfilter and DOSE::setReadable (2018-05-25, Fri)
Changes in version 3.9.1
- change color scheme of dotplot of compareClusterResult back to
red->purple (2018-05-17, Thu)
- https://support.bioconductor.org/p/108996/
Changes in version 3.8.0
- Bioconductor 3.7 release
Changes in version 3.7.1
- uniprot_get function (2018-01-30, Tue)
- import enrichplot (2018-01-29, Mon)