David McGaughey
David McGaughey
# R ``` library(tidyverse) library(RJSONIO) anno % as_tibble() anno_tib %>% dim() ``` This returns 152,392 variants. # bash ``` zcat sample717_SmallVariants.genome.vcf.gz | grep PASS | wc -l ```` This returns...
This feature is already implemented as --show-samples. But this is only available in gemini query, not anything else (automosal_recessive , de_novo, etc.). It would be really useful to quickly see...
Issue in 0.19.0 The gemini variant_id is being printed instead of the rs_id when you run gemini query --format tped. I think the issue is on line 191 for this...
Is there a reason why this filter has been removed from the x_linked_\* tests? This isn't a crucial filter, but I do like to set it for the tests we...
Clinical centers are recommended to check ACMG's incidental finding list (http://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/). It would be useful if Gemini facilitated this kind of query by either building a "Built-in analysis tool" for...
Hi, I've been playing with DESC and I just wanted to make sure I wasn't being stupid about something. DESC does not use batch labels at any point in the...
Would it be possible to allow schex to take data frames / tibbles as input? I work with a lot of huge objects that I largely handle by extracting the...
The snakefile/scripts are heavily hardcoded in two ways: - scripts are assumed to be in ~/git/massive_integrated_eye_scRNA/src/ - the working dir is occasionally hardcoded (in those above scripts mostly) to be...
Dive into each major "category", where category is a cell type (e.g. Cones) and re-run scVI -> clustering to find celltypes within the major cells types (for example there are...
[slingshot](https://bioconductor.org/packages/release/bioc/html/slingshot.html)