Transcription factor enrichment analysis
2
0
Entering edit mode
7.3 years ago
tarek.mohamed ▴ 370

Hi All,

I am working with some RNA-seq and Chip-seq data.

Can you recommend software / R package that can help me perform transcription factor enrichment analysis

Thanks tarek

RNA-Seq ChIP-Seq • 2.3k views
ADD COMMENT
0
Entering edit mode
7.3 years ago
seidel 11k

You can use the edgeR or DESEQ2 packages to find differentially expressed genes from your RNA Seq data, and you can use the GenomicRanges package to slice and dice your ChIP Seq data (assuming you've called peaks). However, you'll have to be a lot more specific with your question to get more specific answers.

ADD COMMENT
0
Entering edit mode

Hi Seidel, Thanks for the reply. I have already done with the RNAseq amd Chipseq analysis. I just wanted to know a tool for transcription factor enrichment analysis.

Tarek

ADD REPLY
0
Entering edit mode
7.3 years ago
dago ★ 2.8k

I have been using RSAT. It contains quite some different tools, and you can work with Chip-seq as well.

ADD COMMENT
0
Entering edit mode

Hi, The link for RSAT is not working! Thanks Tarek

ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode

oups. Now it should work.

ADD REPLY

Login before adding your answer.

Traffic: 1665 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6