Ensembl id to Gene name

Question

[V]

I have a normal count table with columns being the sample names and rows being Ensembl ideas, does anyone know of an easy way that I can convert all of the ensembl ids into official gene names?

Thanks

Answer 1

[igor]

See previous discussion:

• Ensembl ID to Gene Symbol
• Convert GenBank Nocleotide Accession to Gene Symbols

[V]

Thanks Igor,

I meant if there is a tool on R (or a command you might be aware of) that can sort out the rows automatically. Not how to do it manually using a database. Fairly new to R and programming here so a less obtuse answer would be greately appreciated. Or the actual R code. Thanks again.

[igor]

https://bioconductor.org/packages/release/bioc/html/biomaRt.html

Answer 2

[datascientist28]

http://uswest.ensembl.org/biomart/martview/8d0c08f24137867826fc952b01798b1c

Watch the tutorial at the bottom. I think this is what you are looking for

[datascientist28]

Here is a tutorial pdf http://uswest.ensembl.org/info/website/tutorials/biomart_worked_ex.pdf

[V]

Thanks for your help,

Ive looked at all of the tutorials, and all of these essentially show how to generate a new table that has the gene name next to the ensembl id if i'm reading all of this correctly.

What I need is how to convert the column (whose rows are made out of enseml Ids) into a column made up of the gene names, without changing the rest of the columns of the file if that makes sense?

[EagleEye]

My simple suggestion is download the complete annotation from UCSC as mentioned below and merge your count file with the downloaded annotation file using Ensembl id column which is common in both files (this can be done with simple UNIX 'join' command or R 'merge' function).

The UCSC annotation file will have all information like, Ensembl ID, Gene symbols, classification, etc.,

[V]

thank you!!

Sorted it all out by doing some reading on the "merge" function!!

Answer 3

[EagleEye]

A: I need to download a list of all human genes with their respective Esemble gene