R library which takes output from GEMINI and, optionally, peddy and wraps it into a interactive html document.
I've recently added the ability to create a report (sans all the color hyperlinks and colors) directly from a VCF (see below).
The idea to provide a happy medium between GEMINI output piped into less and using a web service like http://vcf.iobio.io.
Click here to see a sample.
The bioinformatician who is running (scripted) GEMINI queries and would like to share results with someone who isn't going to run custom GEMINI queries for their samples.
That said, the document is generated quickly (seconds). The limiting factor is the speed of the GEMINI queries. So it could be used semi-interactively for a command-line skilled analyst who wanted a friendlier output from GEMINI than less and csvkit.
You don't have to hook into a web page which may disappear in x months/years.
This also has the tremendous advantage of being fully portable - you just send the html document to the user and they can use their web browser to study the exome/NGS results for a sample/trio.
Once you have the document it works without internet
Well, that's actually what I have been doing for a few years. The analysts are not super happy, though, because there's a lot of little Google searches they have to keep doing - OMIM, dbSNP, etc. This html document has hyperlinks for common searches.
It also has custom selectable columns and filtering options to quickly do some basic searches (highest CADD, lowest cohort AF, etc.). These are fiddly to do in Excel.
They are included in the package (see below), but also you can click these two:
You can run devtools::install_github('davemcg/see_gem', build_vignettes=T) and read the documentation. Be warned - this is pre-alpha software and functions will change (sometimes dramatically).
Contact me or do a pull request if you have questions, features, or ideas. Or bugs.