In sk-sahu/sig-bio-shiny: Exploration and Significant Biology on a Gene Set.

knitr::opts_chunk$set(echo = FALSE, warning = FALSE)

From AnnotationHub OrgDb

suppressMessages(library(AnnotationHub))
suppressMessages(library(DT))
ah = AnnotationHub()
orgdb <- query(ah, "OrgDb")
df <- as.data.frame(cbind(orgdb$ah_id, orgdb$species, 
                          orgdb$taxonomyid, orgdb$title))
names(df) <- c("AnotationHub ID", "Species", "Taxonomy ID", "Title")
DT::datatable(df)

From KEGG API

All the kegg organism short name got through kegg rest api

source("../R/module_app_input_utils.R")
kegg_list <- kegg_link()
DT::datatable(kegg_list)

sk-sahu/sig-bio-shiny documentation built on June 12, 2020, 8:06 p.m.