How to annotate genes from results of DiffBind
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Chris ▴ 20
@3fdb6f97
Last seen 3 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 • 1.1k views
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@james-w-macdonald-5106
Last seen 48 minutes ago
United States

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

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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.

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