Question

How to annotate genes from results of DiffBind

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Chris ▴ 20

@3fdb6f97

Last seen 4 months ago

United States

Hi all, I looked at the GenomicAlignments package but don't know how. Would you have a suggestion? Thank you so much! I don't know why bioconductor automatically switch to follow by message even thought I chose by email.

ATACSeq • 1.2k views

ADD COMMENT • link updated 20 months ago by James W. MacDonald 67k • written 20 months ago by Chris ▴ 20

score 2 · Accepted Answer · 2023-04-03

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 19 hours ago

United States

You could use GenomicAlignments directly, but I think most people use either ChIPseeker or ChIPpeakAnno instead.

ADD COMMENT • link 20 months ago James W. MacDonald 67k

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Thank you for your suggestion! I tried GenomicAlignments but don't know how after reading its manual. Would you please tell me how? Will try your packages.

ADD REPLY • link 20 months ago Chris ▴ 20

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Both ChIPseeker and ChIPpeakAnno have vignettes showing how to annotate peaks. The ChIPpeakAnno Quick Start vignette get right to the point using the GRanges objects returned by DiffBind.

ADD REPLY • link 20 months ago Rory Stark ★ 5.2k