David McGaughey

Is there any kind of workaround we could implement before this feature gets added? Perhaps some way to get the VEP --pick (https://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html) information added to variant_impact?

Ah, that's cleaner ``` acmg_genes=\'ACTA2\',\'ACTC1\',\'APC\',\'APOB\',\'BRCA1\',\'BRCA2\',\'CACNA1S\',\'COL3A1\',\'DSC2\',\'DSG2\',\'DSP\',\'FBN1\',\'GLA\',\'KCNH2\',\'KCNQ1\',\'LDLR\',\'LMNA\',\'MEN1\',\'MLH1\',\'MSH2\',\'MSH6\',\'MUTYH\',\'MYBPC3\',\'MYH11\',\'MYH7\',\'MYL2\',\'MYL3\',\'MYLK\',\'NF2\',\'PCSK9\',\'PKP2\',\'PMS2\',\'PRKAG2\',\'PTEN\',\'RB1\',\'RET\',\'RYR1\',\'RYR2\',\'SCN5A\',\'SDHAF2\',\'SDHB\',\'SDHC\',\'SDHD\',\'SMAD3\',\'STK11\',\'TGFBR1\',\'TGFBR2\',\'TMEM43\',\'TNNI3\',\'TNNT2\',\'TP53\',\'TPM1\',\'TSC1\',\'TSC2\',\'VHL\',\'WT1\' family_id='your_fam_id' gemini query --header -q "SELECT chrom, start, gene, clinvar_sig, impact, impact_severity, max_aaf_all, (gts).(family_id=='$family_id') FROM variants WHERE \ (gene IN ($acmg_genes) ) \ AND \...

Yes please! I've been using this in my VEP annotations. I was thinking I could just use Gemini's ExAC, then I wondered "wait, what version are they using?" I suggest...

Hmm, I was afraid that might be the case. I was poking around the source code and it didn't look straightforward. In the meantime I'll see what the lightest way...

I'm wondering if you should just make a wrapper to turn a data frame into a `SCE`. The tibble I've been working with is cell (rows) x data (UMAP, genes,...

I believe the only error now is because I haven't set up a `watch` tag. Which I cannot do as I am locked out of my bioc account. I have...

I believe that third party packages are anything not me (so other libraries/packages). Is there better language I should use?

I've tweaked the text (the first block is just for line formatting and a missing space) of the LICENSE. I've simplified the language of the last paragraph. I'm a bit...

I have! Appreciate all the comments - I've been trying to address other work and haven't had time to come back to this. Hoping to address these soon.

0.99.2 pushed which I hope addresses all of the comments (and doesn't create new issues). Happy end of 2023 everyone.