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Question: Transcription factor enrichment analysis
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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

ADD COMMENTlink 2.7 years ago tarek.mohamed • 250 • updated 2.7 years ago dago ♦ 2.5k
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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 COMMENTlink 2.7 years ago seidel 6.8k
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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 REPLYlink 2.7 years ago
tarek.mohamed
• 250
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I have been using RSAT. It contains quite some different tools, and you can work with Chip-seq as well.

ADD COMMENTlink 2.7 years ago dago ♦ 2.5k
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Hi, The link for RSAT is not working! Thanks Tarek

ADD REPLYlink 2.7 years ago
tarek.mohamed
• 250
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oups. Now it should work.

ADD REPLYlink 2.7 years ago
dago
♦ 2.5k

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