Anthony Sonrel

34 posts

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Anthony Sonrel

Anthony Sonrel

@AnthonySonrel

Bioinformatics Scientists @Idorsia Former PhD student in Biostatistics & Bioinformatics @UZH_en.

Zurich, Switzerland Katılım Ağustos 2017
151 Takip Edilen54 Takipçiler
Anthony Sonrel retweetledi
RenkuIO
RenkuIO@RenkuIO·
Couldn't make it to one of our 🫖 talks? No worries, we will be releasing the recordings shortly! At the end of 2021, Almut and Anthony from UZH showed us their set up of a framework for bioinformatics benchmarking! Check it out now: youtu.be/Ia0JxM0u4y4 @SDSCdatascience
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Anthony Sonrel retweetledi
RenkuIO
RenkuIO@RenkuIO·
We are so excited to have Renku champions from the bioinf. community speaking at our next ☕ talk! Almut & Anthony from UZH/SIB will present: "A framework for open and continuous community benchmarking of bioinformatic tools". iCal: shorturl.at/inqIN @SDSCdatascience
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Anthony Sonrel retweetledi
Zoltán Kutalik
Zoltán Kutalik@zkutalik·
Looking forward to hearing your feedback on our approach to decompose different measures of obesity into (4) orthogonal components to better understand their biology and impact on cardio-metabolic health and lifestyle. tinyurl.com/yy3zlqte
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Anthony Sonrel retweetledi
Matthew N. McCall
Matthew N. McCall@matthewnmccall·
#bioc2020 @bioconductor Day 5 (7/31) contributed talk: Bench pressing performant single cell RNA-seq preprocessing tools through pipeComp; a general framework for the evaluation of computational pipelines, presented by @AnthonySonrel
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Anthony Sonrel retweetledi
Rahul Satija
Rahul Satija@satijalab·
The landscape of human cells! From Guoji Guo's lab- single-cell RNA-seq of 500,000 cells across 60 human tissues. Also includes biological replicates, detailed annotation, and open code/data: nature.com/articles/s4158…
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Anthony Sonrel
Anthony Sonrel@AnthonySonrel·
"A unique feature of Capybara is the measurement of cell identity as a continuum (...)" Thank you! We need more of this in cell-type inference. dlvr.it/RQFLCr
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Roman Hillje
Roman Hillje@fakechek1·
@AnthonySonrel @markrobinsonca Thanks for responding so quickly! I noticed that the authors of intrinsicDimension used k = 10 in the examples of the functions. Is that what you used as well?
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Anthony Sonrel
Anthony Sonrel@AnthonySonrel·
@fakechek1 @markrobinsonca Thanks for sharing this interesting observation! I discussed this with PL Germain but I'm afraid we don't have a clear advice on this aspect, as we used a fixed value. That's definitely an aspect we will look at in the future.
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Roman Hillje
Roman Hillje@fakechek1·
@AnthonySonrel @markrobinsonca However, that function itself takes k as an argument. When plotting the result of maxLikGlobalDimEst() over k, I get roughly the same shape as the variability explained by each PC. Do you have advice on how do to choose a proper value for k? Thank you! 2/2
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Anthony Sonrel retweetledi
Mark R@markrobinsonca@{genomic.social,bsky.social}
Mark R@markrobinsonca@{genomic.social,bsky.social}@markrobinsonca·
OK, my current list is 31 scRNA-seq (analysis method) benchmarks: docs.google.com/spreadsheets/d… I consolidated @seandavis12's @_lazappi_'s @JMA_Data's and went through the @GenomeBiology benchmark issue. Any others I missed?
Mark R@markrobinsonca@{genomic.social,bsky.social}@markrobinsonca

Dear #academictwitter, I'm looking for a list of benchmarks for single cell RNA-seq data analysis. Generally, so normalization, DE, clustering, cell assignment, etc. I'm OFC aware of the "Methods comparisons" section in @seandavis12's awesome list (bit.ly/2Rhq1fY) ..

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Anthony Sonrel retweetledi
Saskia Freytag
Saskia Freytag@SaskiaFreytag·
My first paper since joining the @ryanlisterlab presents a tool - schex - that can avoid overplotting in dimension reduction plots of single cell data. For example, schex allows accurate plotting of the expression of CD4 of over 6,000 cells. tinyurl.com/tftu636 1/n
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