Question

Accessing ENCODE data through R

1

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4.8 years ago

salvatore.raieli2 ▴ 90

Hi everyone,

I would like to download some ENCODE data. I want to download which genes present in their promoter the binding of particular Transcription Factor. Starting from a trasncription factor I would like an easy way to retrieve a gene list (not sequences, but more processed data) where they find that Transcription Factor. The best, will be a way to access this data through R.

Thank you for your help

R ENCODE • 1.1k views

ADD COMMENT • link updated 4.8 years ago by ATpoint 82k • written 4.8 years ago by salvatore.raieli2 ▴ 90

1

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Maybe ENCODExplorer package?

ADD REPLY • link 4.8 years ago by zx8754 11k

score 2 · Accepted Answer · 2019-06-27

2

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4.8 years ago

ATpoint 82k

If it is human, try the ReMap database and intersect your regions with it.

ADD COMMENT • link 4.8 years ago by ATpoint 82k

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thank you, I downloaded the bed file for the TF I needed

ADD REPLY • link 4.8 years ago by salvatore.raieli2 ▴ 90