Package: DOSE 4.1.0

Guangchuang Yu

DOSE: Disease Ontology Semantic and Enrichment analysis

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

Authors:Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]

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DOSE.pdf |DOSE.html✨
DOSE/json (API)
NEWS

# Install 'DOSE' in R:

install.packages('DOSE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guangchuangyu/dose/issues

Datasets:

DGN_EXTID2PATHID - Datasets
DGN_PATHID2EXTID - Datasets
DGN_PATHID2NAME - Datasets
NCG_EXTID2PATHID - Datasets
NCG_PATHID2EXTID - Datasets
VDGN_EXTID2PATHID - Datasets
VDGN_PATHID2EXTID - Datasets
VDGN_PATHID2NAME - Datasets
geneList - Datasets

On BioConductor:DOSE-4.1.0(bioc 3.21)DOSE-4.0.0(bioc 3.20)

annotation visualization multiplecomparison genesetenrichment pathways software disease-ontology enrichment-analysis semantic-similarity

15.09 score 118 stars 64 packages 1.9k scripts 29k downloads 138 mentions 24 exports 86 dependencies

Last updated 2 months agofrom:898262a312. Checks:OK: 6 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	OK	Nov 29 2024
R-4.5-linux	ERROR	Nov 29 2024
R-4.4-win	OK	Nov 29 2024
R-4.4-mac	OK	Nov 29 2024
R-4.3-win	OK	Nov 29 2024
R-4.3-mac	OK	Nov 29 2024

Exports:clusterSim doseSim doSim enrichDGN enrichDGNv enrichDO enrichNCG EXTID2NAME facet_grid gene2DO geneID geneInCategory geneSim gseDGN gseDO gseNCG gsfilter mclusterSim parse_ratio setReadable show simplot summary theme_dose

Dependencies:AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools colorspace cowplot cpp11 crayon curl data.table DBI digest fansi farver fastmap fastmatch fgsea formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggplot2 glue GO.db GOSemSim gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp reshape2 rlang RSQLite S4Vectors scales snow stringi stringr sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector yulab.utils zlibbioc

DOSE: Disease Ontology Semantic and Enrichment analysis

Guangchuang Yu

Rendered fromDOSE.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-09-09
Started: 2015-06-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
clusterSim	clusterSim
Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.	compareClusterResult-class plot,compareClusterResult-method show,compareClusterResult-method summary,compareClusterResult-method
compute information content	computeIC
Datasets	DataSet DGN_EXTID2PATHID DGN_PATHID2EXTID DGN_PATHID2NAME geneList NCG_EXTID2PATHID NCG_PATHID2EXTID NCG_PATHID2NAME VDGN_EXTID2PATHID VDGN_PATHID2EXTID VDGN_PATHID2NAME
doseSim	doseSim doSim
Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>)	enrichDGN
enrichDGN	enrichDGNv
DO Enrichment Analysis	enrichDO
enrich.internal	enricher_internal
enrichNCG	enrichNCG
Class "enrichResult" This class represents the result of enrichment analysis.	enrichResult-class show,enrichResult-method summary,enrichResult-method
EXTID2NAME	EXTID2NAME
convert Gene ID to DO Terms	gene2DO
geneID generic	geneID
geneInCategory generic	geneInCategory
geneSim	geneSim
GSEA_internal	GSEA_internal
Class "gseaResult" This class represents the result of GSEA analysis	gseahResult-class gseaResult-class show,gseaResult-method summary,gseaResult-method
DisGeNET Gene Set Enrichment Analysis	gseDGN
DO Gene Set Enrichment Analysis	gseDO
NCG Gene Set Enrichment Analysis	gseNCG
gsfilter	gsfilter
mclusterSim	mclusterSim
parse_ratio	parse_ratio
setReadable	setReadable
show method	show
simplot	simplot
summary method	summary
theme_dose	theme_dose

Package: DOSE 4.1.0

DOSE: Disease Ontology Semantic and Enrichment analysis

DOSE: Disease Ontology Semantic and Enrichment analysis

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)