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.
> 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.