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Alex Wolf proslijedio/la je Tweet
If you're interested in who will be a future scientific leader, keep an eye on the PhD students who highlight, promote, and applaud the work of their competitors.
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Many thanks to the authors of BBKNN from Teichmann Lab (in particular, Krzysztof Polański) for integrating the tool so well into Scanpy and letting us use it as a reference in the tutorial. Here are the original sources: https://github.com/Teichlab/bbknn https://doi.org/10.1093/bioinformatics/btz625 …
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Scanpy 1.4.5 is out with an overhauled website and a long-overdue first tutorial on dataset integration. Most contributions from Scanpy core (
@trueflyingsheep,@ivirshup,@gokcen,@fidel_ramirez) with the "ingest" tool due to@koncopd. https://scanpy.readthedocs.io/en/latest/release-notes.html#version-1-4 …pic.twitter.com/gbFeLEDOA4
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Happy to share a first press release on Cellarity!
#cellbehaviorhttps://www.flagshippioneering.com/press/flagship-pioneering-unveils-cellarity-the-first-company-to-discover-medicines-targeting-cell-behavior …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Alex Wolf proslijedio/la je Tweet
Super happy that our open-source modular toolkit
#scanpy for single cell genomics analyses was selected by@cziscience for funding to expand core infrastructure and build a true community platform. This alongside giants such as#scikit-learn and#numpy.
https://chanzuckerberg.com/newsroom/chan-zuckerberg-initiative-awards-5-million-for-open-source-software-projects-essential-to-science/ …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Alex Wolf proslijedio/la je Tweet
Excited to share our scVelo manuscript - led by
@VolkerBergen and@falexwolf, we generalize the beautiful RNA velocity concept from@KharchenkoLab and@slinnarsson to transient cell states through dynamical modeling. http://www.biorxiv.org/content/10.1101/820936v1 … and http://www.scvelo.org#scRNAseqpic.twitter.com/LuuKjmKbYt
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Alex Wolf proslijedio/la je Tweet
Excited to share our recent work on generative modeling for unpaired data using a ‚transformer VAE’. Led by
@MohammadLotfol1 and@falexwolf, we extend scGen using a conditional VAE together with an MMD regularization. Applications for images and scRNA-seq. http://arxiv.org/abs/1910.01791 pic.twitter.com/Hmt5Ws70ny
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Our (with
@MohammadLotfol1,@MNaghipourfar,@fabian_theis) new end-to-end-trained backend for scGen is out: transformer VAE. Predict how gut cells respond to infection, immune cells to stimulation, or how people would look with a smile (
->
). https://arxiv.org/abs/1910.01791 pic.twitter.com/fAZaxfOff7
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Alex Wolf proslijedio/la je Tweet
Proudly carrying Scanpy decal on my mac, an incredibly useful python package developed by my colleague
@falexwolf. I wish I had such a tool 4 years ago when I was building data integration solutions with Deep Learning.pic.twitter.com/eu8hf6rAjy
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Alex Wolf proslijedio/la je Tweet
Cellarity is hiring both Software Engineers (see
@jejomath 's tweet) and Machine Learning Scientists. see the job post here: https://www.linkedin.com/jobs/search/?currentJobId=1262097201&f_C=29602&keywords=cellarity&locationId=OTHERS.worldwide …https://twitter.com/jejomath/status/1161740804748132354 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Alex Wolf proslijedio/la je Tweet
Happy that our tool scGen just got published in
@naturemethods. We show that generative models predict single-cell perturbation effects out-of-sample - great work led by@MohammadLotfol1 and@falexwolf! Try it at http://github.com/theislab/scgen , read at http://nature.com/articles/s41592-019-0494-8 …pic.twitter.com/l2FFUq2HSe
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There now is a press release of @HelmholtzMucEn on
@GenomeBiology's PAGA paper (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x …): https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/46175/index.html …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
"Overall, we found a large diversity across the four evaluation criteria, with only a few methods, such as PAGA, Slingshot, and SCORPIUS, performing well across the board (Fig. 2b)."
From the TI review https://www.nature.com/articles/s41587-019-0071-9 … about https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x …https://twitter.com/saeyslab/status/1112739063671472128 …
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Alex Wolf proslijedio/la je Tweet
Unsure which of the more than 70 trajectory inference method to use for your single-cell dataset? The benchmarking effort led by
@rcannood and@zouters is now published at https://www.nature.com/articles/s41587-019-0071-9 ….pic.twitter.com/cwbhw8EMcR
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Alex Wolf proslijedio/la je Tweet
Awesome talk by David on pseudodynamics and diffxpy. Finally a malleable differential expression toolbox for python!https://twitter.com/singlecellomics/status/1110834112795996160 …
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Alex Wolf proslijedio/la je Tweet
Using PAGA,
@LickertHeiko elucidates the origin of pancreatic beta cells, which are crucial for producing insulin, in an STZ mouse model of diabetes#SCOGmunich2019 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x …pic.twitter.com/2FtIwsaLuH
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Since today, Scanpy has a logo with a cellular decomposition of a Scampi in it.
http://scanpy.rtfd.io pic.twitter.com/6uiSLGL3pW
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Alex Wolf proslijedio/la je TweetHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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Alex Wolf proslijedio/la je Tweet
A view in log scale of the
@github metrics of the software for#singlecell#omics analysis, with SCANPY clearly in the lead http://bit.ly/softscell pic.twitter.com/wVLRUMMd18
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Needless to say, that all of it is conveniently available in Scanpy, e.g., through `http://sc.tl .paga`, `http://sc.pl .paga`, `http://sc.tl .draw_graph(adata, init_pos='paga')`, `http://sc.tl .umap(adata, init_pos='paga')`.
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