Carlo SF

347 posts

Carlo SF

Carlo SF

@CharlesColdroom

ML+AI for Translational Medicine & Spatial Biology

London, England Tham gia Temmuz 2014
539 Đang theo dõi249 Người theo dõi
Carlo SF đã retweet
Lukas Valihrach
Lukas Valihrach@LukasValihrach·
Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia cell.com/cell-reports/f…
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Luciano Martelotto 🛠🧬💻🇦🇺
Luciano Martelotto 🛠🧬💻🇦🇺@LGMartelotto·
What spatial subcellular resolution RNA technologies would you love to have in your lab right now? No questions asked…well, maybe a few 😎. Plz repost
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Carlo SF
Carlo SF@CharlesColdroom·
@tunguz The Boddickers? Loved their Detroit concerts.
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Bojan Tunguz
Bojan Tunguz@tunguz·
I bet you can’t.
Bojan Tunguz tweet media
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Peter Androvič
Peter Androvič@AndrovicPeter·
So happy to see my first postdoctoral work now published @NatureComms. We devised a new approach integrating single cell spatial transcriptomics by #MERFISH with electron microscopy imaging, and used it to probe cellular responses to demyelination nature.com/articles/s4146…
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Carlo SF
Carlo SF@CharlesColdroom·
@ozgungokce Congratulations Ozgun! Best wishes to you and the lab!
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Ozgun Gokce
Ozgun Gokce@ozgungokce·
I’m happy to share that I started a new position as Professor at University Bonn, UKB. We will continue to harness Big Data & Omics to illuminate the Brain and Body.
GIF
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Carlo SF
Carlo SF@CharlesColdroom·
@BlindTasters @tereza_roux It ought to be in Naturalis history - in one book of this collection he wrote at length about wines.
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Wine Blind Tasting
Wine Blind Tasting@BlindTasters·
Thanks to @tereza_roux for pointing out that Pliny the Elder (d. 79 CE) wrote about grape varieties that 'are not harvested until it has frozen'. Can anyone provide the exact reference? twitter.com/BlindTasters/s…
Wine Blind Tasting@BlindTasters

I wonder how the practice of making ice wine began. Did someone suddenly wake up at 3am and say, "Hey, it's -8 degrees, let's go harvest those left-over grapes from our steep vineyards and see if we can press them!" @WinesofGermany

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Carlo SF
Carlo SF@CharlesColdroom·
@rmassonix Indeed, lots of data structures, which make inter-conversion difficult or extremely complicated for R-based analysis.
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Ramon Massoni Badosa
Ramon Massoni Badosa@rmassonix·
Hence, if I want to run ArchR's TF footprinting analysis from a Seurat object I basically need to start my analysis from scratch. Instead of converging into universal data structures, R-based ecosystems are diverging more and more as technology progresses.
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Ramon Massoni Badosa
Ramon Massoni Badosa@rmassonix·
R #rstats is by far the best language to analyse single-cell genomics data. However, in a year or so everyone will have transitioned to Python. These are top reasons why this will happen:
Daniela Witten@daniela_witten

do you prefer to bang your head against a brick wall for hours trying to figure out how to subset your data matrix in a language that LITERALLY IS NOT DESIGNED FOR DATA ANALYSIS??? Both options are equally valid! It’s a matter of personal preference!!!

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Carlo SF
Carlo SF@CharlesColdroom·
@timtriche @mikelove @rmassonix IMHO, Seurat is popular because of detailed, user-friendly (also for beginners) vignettes. It offers lots of useful visualisation functions and explains how to use them in a language accessible also by non-bioinformaticians.
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Carlo SF
Carlo SF@CharlesColdroom·
@LGMartelotto One thing to consider: the Parse kit does not require instruments, so can be readily used in P3 labs and/or with nasty samples that you really do not want to contaminate the Chromium.
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Luciano Martelotto 🛠🧬💻🇦🇺
Luciano Martelotto 🛠🧬💻🇦🇺@LGMartelotto·
In summary: -Parse is the first serious contender but the Force is still is way too strong in 10x. Fear not my talented Padawans. -for me the choice it’s been easier: 10x solutions span across multiple areas I need (ATAC, multi-ome, T/BCR-seq, CRISPR, BEAM-T, CITE-seq etc, etc)
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Luciano Martelotto 🛠🧬💻🇦🇺
Luciano Martelotto 🛠🧬💻🇦🇺@LGMartelotto·
@ParseBio versus @10xGenomics done at @HutchInnovation A very nice sequel to our similar experience at HMS that you can find here: twitter.com/lgmartelotto/s… Cell loss/capture rate sensitivity and costs of sequencing (need a 200 cycle kit in Parse) are key things to consider.
Fred Hutch Innovation Lab@HutchInnovation

One of goals at the Fred Hutch Innovation lab is to assess interesting new single cell sequencing methods. We tested Parse Bio’s WTA kit on human PBMCs, sequenced all libraries and analyzed the data. Here our our preliminary findings: (1/9)

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Luciano Martelotto 🛠🧬💻🇦🇺
Luciano Martelotto 🛠🧬💻🇦🇺@LGMartelotto·
Plus…and perhaps the most important one to me, is Customer support. 10x, in my opinion, is unbeatable at this. I’ve been lucky but I don’t recall one issue it wasn’t resolved since I started using 10x kits in Jan 2017.
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Khám phá

@LGMartelotto @tunguz @AndrovicPeter @jdpereira @NatureComms @ozgungokce @BlindTasters @tereza_roux