igor comments

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                                            igor

readTranscriptFeatures with GTF

I understand that the BED and GTF files are different. I wanted to see if there was a way to achieve the same annotation results from both. It sounds like...

readTranscriptFeatures with GTF

Thanks for clarifying. I was hoping all or some parts were already included in the package. It would be a nice feature to have.

Port IndelRealignment pipeline

There haven't been any comments here for about 3 years. Have there been any updates in a separate thread or offline? Is there any hope there may be any eventually?

bulk_clones plot "CNV state" legend colors

Thanks for the update! I had some other packages break with ggplot2 3.5.0 as well.

ggsave does not work with ggsurvplot objects anymore

The `ggsave` option does not work anymore for me either. This may be an R 4.1 issue, but I have not investigated. In the meantime, you can try an alternate...

2023 update?

Yes, I plan to update. My last submission to CRAN was rejected and I have to restructure the code to comply with CRAN policies. I just haven't had time to...

Accessing Mouse MSigDB Collections

Thank you for the suggestion. This is definitely a possibility. See also: https://github.com/igordot/msigdbr/issues/25

Problem with dyplr dependency (I think)

I am not seeing this error with the latest CRAN version of msigdbr. I notice you have some other packages loaded. Do you still get this error if you only...

First release of Mouse MSigDB (v2022.1.Mm)

I am not yet sure what the optimal way to handle the mouse MSigDB would be. For example, maybe it should be a separate package. The package currently stores all...

Save the 'entrez_gene' columns in character mode

Thank you for the suggestion. I don't usually work with Entrez IDs. I didn't notice that Bioconductor annotation packages treat them as characters. I assume it's to be consistent with...