ls_annotables: List Annotation Tables from 'annotables' package

In IDConverter: Convert Identifiers in Biological Databases

List Annotation Tables from annotables package

Description

The tables are obtained from annotables package and stored in Zenodo for better management. They can be downloaded and loaded with load_data(). See details for more info.

Usage

ls_annotables()

Details

Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, biomaRt does this for you, but users may get tired of remembering biomaRt syntax and hammering Ensembl's servers every time. These tables have basic annotation information from Ensembl Genes for:

• Human build 38 (grch38)

• Human build 37 (grch37)

• Mouse (grcm38)

• Rat (rnor6)

• Chicken (galgal5)

• Worm (wbcel235)

• Fly (bdgp6)

• Macaque (mmul801) Where each table contains:

• ensgene: Ensembl gene ID

• entrez: Entrez gene ID

• symbol: Gene symbol

• chr: Chromosome

• start: Start

• end: End

• strand: Strand

• biotype: Protein coding, pseudogene, mitochondrial tRNA, etc.

• description: Full gene name/description Additionally, there are tx2gene tables that link Ensembl gene IDs to Ensembl transcript IDs.

NOTE, the description above is copied from README of annotables package. If you are unclear to the data tables, please refer to annotables.

Value

a data.frame

References

https://github.com/stephenturner/annotables

Examples

ls_annotables()
load_data(ls_annotables()[1])

IDConverter documentation built on March 31, 2023, 10:25 p.m.