Metagene Analysis in R - Best Options?
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vanbelj ▴ 10
@vanbelj-21216
Last seen 14 days ago
United States

What packages are commonly used for metagene analysis in R? I'm interested in taking DE genes identified from DESeq2 and making metagene plots from bam files across promoter and CDS regions.

I tried using metagene2, but it keeps throwing an error. DESeq is not listed as a dependency for metagene2, and since it's call DESeq vs. DESeq2, I'm guessing metagene2 isn't being maintained? I posted the issue on the maintainer's github, but looking for alternatives in the meantime.

Thanks!

> library(metagene2)
Loading required package: R6
Loading required package: BiocParallel
Error: package or namespace load failed for ‘metagene2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘DESeq’

It looks like someone else has also had this problem: post

The package maintainer was responsive to my comment on Github. Once it's figured out, I will post the resolution on this thread in case others have the same problem in the future.

metagene2 • 267 views
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vanbelj ▴ 10
@vanbelj-21216
Last seen 14 days ago
United States

The package maintainer identified the issue and a functional version should be downloadable from Bioconductor starting tomorrow 3/17/21. I downloaded from source and the error no longer occurs, so I assume the fix will work once Bioconductor has updated (should be tomorrow morning).

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