Daniel Cook ∛

My name is Dan

[Kishwar @kishwarshafin]

DeepSomatic (https://t.co/BqZkDNMv1E) preprint is out showing improvements in somatic variant calling in various platforms.

Work lead by @jiimiinpaark and @daniel_e_cook. Tumor-only lead by @pichuan. In collaboration with @acarroll_ATG, @MishaKolmogorov and @BenedictPaten. 🧵1/7

[Daniel Cook ∛ @daniel_e_cook]

@T1MD1 @fulcrumgenomics Congrats Tim - sounds like a great new role!

[Daniel Cook ∛ @daniel_e_cook]

@d0m96 https://t.co/MAGfNOJ5EP works well. Supports more complex operations (log, exp, etc) if you prefix your calculation with ‘=‘. Has a history and clipboard support.

[Daniel Cook ∛ @daniel_e_cook]

@XLR For me, it’s 0.38 or nothing! https://t.co/3l8UlsqheZ

[Daniel Cook ∛ @daniel_e_cook]

@daniel_c0deb0t @AnthropicAI Congrats and best of luck in your new role! I look forward to seeing what you will do next!!

[Daniel Cook ∛ @daniel_e_cook]

@daniel_c0deb0t latex? I had this problem recently. It took me at least 4 hours to figure out.

[Daniel Cook ∛ @daniel_e_cook]

@aarondfrancis There are two sets of twins in my family. One identical and one fraternal. It’s fun because I can say I have 3 twin brothers. Good luck!

[Daniel Cook ∛ @daniel_e_cook]

@zamanian_ Congrats!!!

[Daniel Cook ∛ @daniel_e_cook]

@shaneenz28 Congrats!!!

[Daniel Cook ∛ @daniel_e_cook]

@karpathy I prefer:

`import IPython; IPython.embed(user_ns=dict(globals(), **locals()))`

Which gives an ipython interpreter.

[Daniel Cook ∛ @daniel_e_cook]

@aaronquinlan what the golf? is fun!

[Daniel Liu @daniel_c0deb0t]

This @rustlang tool is part of my work @GoogleHealth’s genomics team (hosts: @daniel_e_cook and @belyaeva_ana). We use it for evaluating DeepConsensus, though it should be generally useful for evaluating basecalling or other sequencing methods

Github: https://t.co/AhUvrBYw5v

[Daniel Cook ∛ @daniel_e_cook]

@ChiBuildings Is it a wood fired pizza place?

[Daniel Cook ∛ @daniel_e_cook]

@vsbuffalo @BioMickWatson @pmelsted @GuillaumOleSan Laughed so hard at this @vsbuffalo

[Vince Buffalo @vsbuffalo]

@BioMickWatson @pmelsted @GuillaumOleSan Yes, Jesus is 1-based too since there is no year zero between 1 BC and 1 AD https://t.co/YtQ9cdttKs.

[Daniel Cook ∛ @daniel_e_cook]

@ChiBuildings “A more welcoming atmosphere.” Not sure the layout was the issue 😆

[Daniel Cook ∛ @daniel_e_cook]

@brent_p It can be helpful to record software versions to a file when using many conda environments for data provenance purposes.

[Daniel Cook ∛ @daniel_e_cook]

@brent_p @brent_p This is the approach I take generally. I tried to create a general purpose environment but too many dependencies clashed. This works well in the context of Nextflow, and I also use conda within Docker for convenience.

[Daniel Cook ∛ @daniel_e_cook]

@brent_p @brent_p Looks great! I like to allow users to set the output dir. e.g.

publishDir "${params.output_dir}/gvcfs"