Anthony Sonrel

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

[[BC]2 @BC2Conference]

@zkutalik @GfellerD @P_Palagi @marc_rr @gardeux_vincent @AiswwaryaPrasad @EPFL_en @CHUVLausanne @unil 💡Discover Omnibenchmark at [BC]2, a modular & extensible framework designed to connect data, methods & metric modules via a #knowledgegraph tracking #metadata.

🎤Presenters: Almut Lütge & Antony Sonrel (@UZH_en)

👉Register: https://t.co/20LusCvCoD
#Bioinformatics #tutorial

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Benchmarking!

Was nice to get a mention of some of our work in this article ..

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

So, this came out ..

[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: https://t.co/VgSfp2Zdf8

@SDSCdatascience

[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: https://t.co/0trSCEuTtI

@SDSCdatascience

[Zoltán Kutalik @zkutalik]

After a long journey our work on PCA-MR (and its application to obesity traits) has found its home: https://t.co/98D2qw0jzV Thanks to the team effort: @jonathan_sulc @AnthonySonrel @Nin0nM @CAuwerx @MarouliEirini @LizaMGD @BogdanDraganski @tuomaskilpela @Peterkjoshi & Ruth Loos

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Ever been frustrated doing QC of your single cell (RNA-seq) data? .. especially when you expect to have rare celltypes?

Check out SampleQC ..
https://t.co/MnaQnYnLhf

(n.b.: thread drafted by @willmacnair)

[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. https://t.co/bF6MwREszN

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

@AnthonySonrel @mikelove pipeComp was published today:
https://t.co/ouG17XFGqM

[Michael Love @mikelove]

Anthony Sonrel @AnthonySonrel on pipeComp, a framework for the evaluation of computational pipelines, with Pierre-Luc Germain and @markrobinsonca at #BioC2020

📦 - https://t.co/iapmOqPlKj
📜 - https://t.co/Yr8z0lLdHZ

[Anthony Sonrel @AnthonySonrel]

@mikelove @markrobinsonca Thanks for sharing the links 😉 forgot to add them in the chat of the conference. Also, the link to the github of pipeComp; https://t.co/1nYdwB3QSL

[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

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Are you an early career researcher (in Europe)?

Please give your feedback to the @EU_Commission on their up-and-coming open publishing platform, ORE (Open Research Europe).

https://t.co/CZMAf7DZQw

#OpenScience
#openaccess

[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: https://t.co/1rOQdbWx6I

[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. https://t.co/eKRgrviDvW

[Anthony Sonrel @AnthonySonrel]

@fakechek1 We increased it a bit, to k=20.

[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.

[Anthony Sonrel @AnthonySonrel]

Are you looking for recommendations of tools in scRNA-seq ? Then our preprint is for you! First collaboration within @markrobinsonca 's group. Props to PL Germain for the idea and the implementation of 'pipeComp'.

[bioRxiv @biorxivpreprint]

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single-cell RNA-seq preprocessing tools https://t.co/uTVGmCd46w #bioRxiv

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

OK, my current list is 31 scRNA-seq (analysis method) benchmarks:
https://t.co/gfan8Kupcp

I consolidated @seandavis12's @_lazappi_'s @JMA_Data's and went through the @GenomeBiology benchmark issue.

Any others I missed?

[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.
https://t.co/zpsS1v550c
1/n