README.md

In guokai8/bioAnno: Build Annotation From Online Database

bioAnno

Build Annotation package by using information from KEGG, NCBI, Ensembl and return OrgDb object such as org.Hs.eg.db. The bioAnno package support all organisms list in Ensembl, KEGG, NCBI.

Description

With the increasing of high throughput data generated, the requirement for having annotation package ready is necessary for people doing functional enrichment analysis, id conversion and other type related analysis. bioAnno provide wrap functions include fromKEGG, fromEnsembl, fromNCBI and fromAnnoHub to build annotation package. And you can easily to build annotation package with the KEGG species code (except fromEnsembl which require scientific name).

Installation

library(devtools)
install_github("guokai8/bioAnno")

Software Usage

library(bioAnno)
## build Annotation package by using fromKEGG
fromKEGG(species="hsa")
## which will build and install package "org.hsa.eg.db" which will include KEGG, GO annotation 
## build Annotation package by using fromEnsembl 
fromEnsembl(species="Human")    
## build from AnnotationHub   
fromAnnHub(species="human")

2.4 Main Functions

-- fromKEGG build annotation package by extracting annotation information from Kyoto Encyclopedia of Genes and Genomes database (KEGG). You can use kegg species code as query species name.

-- fromNCBI build annotation package by extracting annotation information from NCBI database.

-- fromENSEMBL build annotation package by extracting annotation information fromENSEMBL database. It includes function to build annotaion package for plant with parameter plant = TRUE

-- fromAnnhub build annotation package with the AnnotationHub package

-- mergeDB merge two annotation packages

Note

The bioAnno provide wrap function which help me to easily build annotation package.

Contact information

For any questions please contact [e-mail]

guokai8/bioAnno documentation built on May 8, 2023, 12:42 p.m.