Robert Allaway
Robert Allaway
I experienced this as well for --esp_af. I don't believe --af_gnomad is deprecated but vep 107 failed to recognize the --af_esp flag and threw an error. I made a small...
(I now see that someone already filed a PR with the same change in #324). For the record, this is the error message I see: ``` (base) bash-4.2# perl vcf2maf.pl...
Hello @jingydz, you can fix this using the `--vep-path` parameter. For example, if you installed vep into a conda environment you could run: `find /. -name '*vep*'` to locate vep....
Hi there, I'm Robert Allaway, a PhD candidate in Yolanda Sanchez' lab at Dartmouth College. I'm currently a bench scientist/cancer biologist studying tumors related to neurofibromatosis type 1 and RAS...
No worries @dhimmel - cheers!
One more potential use case that differs slightly in input/output from the last. Let me know if this is within the scope of this project: I have a list of...
I also have this issue with the latest BioC release.
FYI, a simple fix is to do something like this (in your example): ``` EnhancedVolcano(res, lab = res$X_1, x = 'log2FoldChange', y = 'padj') ``` Note that this might not...
Dear Jianfeng, Thank you for the help! That makes sense. I'll make sure sqlite3 is in my path. In the interim, I used the perl version on the command line,...
Hello, I wanted to re-surface this issue. We have many use cases for Attribution requirements and it would be great if this could be added to DUO. I am happy...