Eric Talevich

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Eric Talevich

Eric Talevich

@etalevich

San Francisco, CA Beigetreten Mart 2010
292 Folgt324 Follower
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Eric Talevich
Eric Talevich@etalevich·
Reach out if you'd like to discuss how we can work together! Experience and services in: - Bioinformatics algorithm development, pipelines, data architecture - Cancer biology, infectious & autoimmune diseases, population genetics, multi-omics - Technical strategy & solutions
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Eric Talevich
Eric Talevich@etalevich·
CNVkit v0.9.10 is out! github.com/etal/cnvkit/re… New plotting features, better GISTIC support, and many bug fixes and infrastructure improvements. Much thanks to contributors over the past ~2 years.
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Goncalo Abecasis
Goncalo Abecasis@gabecasis·
If you could read the DNA of half a million people, would you do it and why? Would it work? What would you learn? To answer this and several related questions, let me walk you through the work my @RegeneronDNA colleagues just published in Nature. 1/24 nature.com/articles/s4158…
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Jeremy Leipzig
Jeremy Leipzig@jermdemo·
If you're interested in trying @nf_core in the context of reproducible peer review I am looking for a participant for a short survey and a test of robustness on disputed m6a paper. $250 recompense. Please DM me for details.
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Eric Talevich
Eric Talevich@etalevich·
@rlim_Hsapiens @biocrusoe Not personally, but I understand it's basically an extension of Parquet and will work in the same scenarios, plus a few more.
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Eric Talevich
Eric Talevich@etalevich·
R has a number of packages that are just datasets, not code. Has this been tried with conda or other package managers in order to make datasets versioned and traceable?
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Eric Talevich
Eric Talevich@etalevich·
@jermdemo Thanks! This is what I was thinking of, nicely integrated with workflows.
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Eric Talevich
Eric Talevich@etalevich·
@dpryan79 Thanks. This would be for derived or accruing datasets that downstream pipelines then depend on, e.g. I've validated a pipeline with RefGene from <date>, and want to pin all its dependencies in code. The data itself doesn't even need to be copied, necessarily.
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Devon Ryan
Devon Ryan@dpryan79·
@etalevich Conda has versions of the Bioconductor experimental dataset packages, so technically yes. However I think you're better off with something like a zenodo DOI for datasets, unless they really require association with non-dataset objects. The thing is most datasets aren't updated.
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ChristofferFlensburg
ChristofferFlensburg@CFlensburg·
You can now link reviews from the preprint on biorxiv. Another step towards a journal-free open science utopia with preprint and post publication peer review. :D connect.biorxiv.org/eval/?platform…
ChristofferFlensburg tweet media
John Inglis@JohnRInglis

Smartly spotted by @PracheeAC -a new @biorxivpreprint feature from our tech wizards Ted and Michael. Links to a list of peer reviewed preprints can be found on each subject category specific page. Featuring reviews from @eLife, @ReviewCommons, and @EMBOPress

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Eric Talevich
Eric Talevich@etalevich·
R has a number of packages that are just datasets, not code. Is there a similar channel/repo in #conda / #anaconda? Guidelines, experiences?
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Eric Talevich
Eric Talevich@etalevich·
I'm hiring for the Data Core at @KariusInc! jobs.lever.co/kariusdx/7b209… We mine biological datasets to power a cfDNA test for infectious diseases. We discover new things every day. HQ is in the Bay Area; remote is also fine.
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Eric Talevich
Eric Talevich@etalevich·
The Karius test works for clinical diagnosis of infectious diseases: kariusdx.com/products/kariu… What's next? We'll go beyond n-of-1, improve the assay itself and its clinical validity, use the assay to make discoveries, and much more.
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Eric Talevich
Eric Talevich@etalevich·
Open source software experience and scientific community engagement would be great. We're looking to work with the global community to bring new discoveries into the open. Again, we've seen things in the blood microbiome that no one else has.
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CCDD at Harvard Chan
CCDD at Harvard Chan@CCDD_HSPH·
TODAY @ 3PM ET: Join @mlipsitch and other experts for The Science of Herd Immunity. They will explain the science of and misconceptions around herd immunity and discuss new research frontiers in immunology, infectious disease dynamics, and human behavior. stanford.io/3cYX2IZ
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Eric Talevich
Eric Talevich@etalevich·
I'm now at @KariusInc ! We have a lifesaving noninvasive test for infectious diseases, and from another perspective, a metagenomic cfDNA assay that works as a powerful new molecular microscope for understanding human physiology.
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Entdecken

@RegeneronDNA @tskir1 @nf_core @jermdemo @dpryan79 @incluzion @KariusInc @AwarenessBites