David Cook @DavidPCook Twitter profile

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David Cook

8 months

Excited to announce the Cook Lab will be opening at the Ottawa Hospital Research Institute Jan 2024. We'll be focusing on intratumoural heterogeneity and therapy resistance in ovarian cancer Eager to work more with the ovarian cancer research community!

Cook Lab

www.cooklab.ca

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David Cook

@DavidPCook

4 years

Thrilled to see that our paper using MULTI-seq to compare transcriptional dynamics of the EMT across contexts is now up on @NatureComms . scRNA-seq of 12 EMT time courses (4 lines, 3 inducers) and screened effects of 22 kinase inhibitors on each combination

Context specificity of the EMT transcriptional response

Nature Communications - It is unclear if a common EMT expression program exists. Here, the authors perform multiplexed single-cell RNA sequencing across 12 EMT time courses and 16 kinase inhibitor...

www.nature.com

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David Cook

@DavidPCook

3 years

Excited my work with @bvanderhyden is out today in @ScienceAdvances ! We took scRNA-seq data of 266 tumors from 8 cancer types, identified & compared expression programs associated with epithelial-mesenchymal plasticity. @uOttawaMed @OttawaHospital

Transcriptional census of epithelial-mesenchymal plasticity in cancer

Epithelial-mesenchymal plasticity is a prevalent source of intratumoral heterogeneity, driven by diverse molecular programs.

www.science.org

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David Cook

@DavidPCook

3 years

Excited to share some new work w/ @bvanderhyden . Used archetypal analysis to learn features of epithelial-mesenchymal plasticity from scRNA-seq data of 160 tumours spanning 8 cancer types. Transcriptional census of epithelial-mesenchymal plasticitiy:

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David Cook

@DavidPCook

2 years

See this often enough that I think it warrants a tweet. Be aware that if you feed Seurat's FeaturePlot >2 custom colors, the values in the plot's scale no longer reflect normalized counts. Can add ggplot2 code to get around this is you still want to use FeaturePlot

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David Cook

@DavidPCook

5 years

Excited to share this work! We wanted to compare the transcriptional dynamics of the EMT across contexts, so we used MULTI-seq to generate scRNA-seq data for 12 EMT time courses and 16 kinase inhibitor screens. With replicates, 960 samples in total.

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David Cook

@DavidPCook

8 months

Excited to share our comparison of Xenium and CosMx data! I feel like a lot of labs/core facilities have made similar observations internally, so we're really glad to put this out for the broader community. 1/n

Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with...

www.biorxiv.org

Luciano Martelotto 🛠🧬💻🇦🇺

@LGMartelotto

8 months

I’m going to quietly leave this here…but not without a shoutout to @DavidPCook , @kirkbjensen and @Kellieiswise for their AMAZING work. 🙌 A Comparative Analysis of Imaging-Based Spatial Transcriptomics Platforms

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David Cook

@DavidPCook

9 months

Great that we're starting to see some data comparing these platforms head-to-head. And kudos to those making the data public. I think we do a disservice trying to boil the comparison down to a couple summary metrics. Eg. dove into this breast cancer data for an hour 1/n

Brant Bassam

@BrantBassamPhD

9 months

@LGMartelotto , further to our conversation comparing $TXG 10X Genomics Xenium and $NSTG NanoString CosMx Spatial Molecular Imager for spatial transcriptomics (ST), we have new data to consider from the lab of Dr Yutaka Suzuki from the University of Tokyo. Dr Suzuki has long been

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David Cook

@DavidPCook

6 years

Wowow! Mapping the Mouse Cell Atlas by Microwell-Seq. scRNA-Seq of >400k cells spanning >50 tissues.

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David Cook

@DavidPCook

6 years

Before and After. Making model figs. Good thing my vector drawing skills are better than my doodling abilities

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David Cook

@DavidPCook

3 years

Thrilled to announce that I've received a #BantingCanada fellowship from @CIHR_IRSC . Excited to be working on cell plasticity with Jeff Wrana at the Lunenfeld-Tanenbaum Research Institute @SinaiHealth .

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David Cook

@DavidPCook

3 years

Successful thesis defense out of the way! @bvanderhyden , thanks for such an incredible PhD experience. And thanks to @ItaiYanai and my other evaluators for taking the time to read my work and give thoughtful feedback. Shame we couldn’t celebrate in person!

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David Cook

@DavidPCook

7 years

Having fun with the Tabula Muris @10xgenomics datasets in scanpy. 55k cells runs smoothly on laptop. Force-directed graph of 12 tissues looks like some abstract art

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David Cook

@DavidPCook

4 years

Thank you 🙏. Definitely an honour to receive the Worton Researcher in Training Award. Couldn’t have done any of it without the supportive environment at @OttawaHospital / @uOttawaMed or my fantastic colleagues and mentors (a particularly special thanks to @bvanderhyden )

The Ottawa Hospital

@OttawaHospital

4 years

Congratulations to @DavidPCook on receiving the Worton Researcher in Training Award in recognition of his outstanding #cancer research achievements and pioneering new techniques! Learn how this rock star researcher uses big data to answer big questions:

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David Cook

@DavidPCook

3 years

Great perspective from the @fabian_theis group on machine learning for perturbational single-cell genomics. Parts about learning a perturbation latent space remind me of Cleary/Regev's points about value of designing random experiments for inference

Machine learning for perturbational single-cell omics

Single-cell data from perturbation experiments enable the use of deep learning approaches to characterize perturbed cellular phenotypes and predict drug properties and effects of treatment. We first...

www.cell.com

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David Cook

@DavidPCook

6 years

Lucky socks for a day of processing single-cell samples. Hopefully they work! Thanks for the hook-up @cirettiwT @10xgenomics !

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David Cook

@DavidPCook

9 months

Excited to talk about this. I came to this project just trying to inform myself to help my institutes with purchase decisions. I have no inherent bias for either platform (and they certainly don’t pay me 🙃). Just want to provide transparent, practical insight into the data

10x Genomics

@10xGenomics

9 months

#Singlecellspatial imaging technologies empower new insights—but how do the different platforms stack up? Find out in a webinar where leading spatial researchers compared Xenium In Situ and NanoString CosMx and see which came out on top in their hands:

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David Cook

@DavidPCook

4 years

Multimodal Analysis of Composition and Spatial Architecture of Human Squamous Cell Carcinoma. scRNA-seq + spatial transcriptomics + in vivo CRISPR screening of SCC xenographs. Very cool work.

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David Cook

@DavidPCook

5 years

Never too many scRNA-seq samples! Using MULTI-seq to run 384 samples across four 10x channels this afternoon

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David Cook

@DavidPCook

3 years

@arjunrajlab I find lazy critique like this is getting reinforced in grad classes. Told to evaluate a paper and get marked for participating in discussion. Everyone scrambles to find anything to say (stats, replicates, protein vs rna) and come to believe that this is how to critique papers

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David Cook

@DavidPCook

3 years

Single-cell folks! Any suggestions for approaching multiome sample prep for large, staggered batches of organoids? ~20 samples per timepoint. Recommendations for fix(?), freeze, and parallel processing (v-bottom plate hacks or something?) appreciated! CC @LGMartelotto @Sc_Ninjas

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David Cook

@DavidPCook

2 years

Head-to-head alignment of some new data with new cellranger update. Comparing v6 and v7 default, as well as the optimized mm10 reference from @Allan_HPool . Median gene ~600 higher. Median UMI ~3k higher. Curious about gene-level diffs with optimized ref.

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David Cook

@DavidPCook

5 years

tSneeze. Ten 96-plex scRNA-seq samples, multiplexed with MULTI-seq

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David Cook

@DavidPCook

4 years

If anyone is using the Seurat + Monocle wrapper vignette as a reference for their own trajectory inference, be cautious how the assays are being transferred. In the vignette, after seurat > CDS > seurat, the original integrated assay gets put into "RNA"

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David Cook

@DavidPCook

9 years

Soooo…I just won $10,000 from the @newhot899 Hot Hit contest!!!!!!! O_O Still shaking

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David Cook

@DavidPCook

3 years

@achamess @LGMartelotto @tangming2005 Usually have key questions at the onset to point, but usually goes 1) freestyle exploration in different directions that seem interesting, 2) scripts become wildly disorganized, 3) burn it down, re-write everything in some logical order based on interesting angles from (1)

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David Cook

@DavidPCook

5 years

Gene expression changes in response to a stimulus are often interpreted as a change in "cell state". Wonder how often exp changes are to *maintain* cell function under different environmental pressures. Don't know of any examples, but interesting thought. Still a "state" change?

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David Cook

@DavidPCook

6 years

Hexbinning gene expression on scRNA-seq embeddings is a nice way to smooth out noisy/sparse signal for visualizations, particularly when the embeddings are heavily overplotted.

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David Cook

@DavidPCook

5 years

Have to sport the @10xGenomics swag while on vacation in Cuba

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David Cook

@DavidPCook

4 years

Beautiful work. Really want to work with joint data like this. Chromatin state change precedes gene expression. Incongruence of profiles can be used to predict cells' future state. Congrats @maple1989 et al!

Sai Ma

@saima_lab

4 years

Does chromatin and gene expression define the same cell states? To answer this, we developed a new technology, SHARE-seq to bring measurements of regulatory mechanisms to single cells.

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David Cook

@DavidPCook

6 years

The last minute scramble to get some RNA Velocity data into the @10xgenomics seminar Friday at the Ottawa Hospital Research Institute.

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David Cook

@DavidPCook

5 years

For visualizing subtle shifts in an embedding. Toying around with visualizing diff in density estimates between two conditions. Kind of an exaggerated example, but could be a cool way to see diffs in one plot instead of 2-color dot confetti. Also controls for diff cell counts

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David Cook

@DavidPCook

5 years

Had a lot of fun working on this with @IvanaMizikova and @HurskainenMaria from @LabThebaud ! Used MULTI-seq for scRNA-seq on 36 mouse lung samples throughout normal and impaired late lung development. BPD is associated with progressive phenotypic changes in all cell types

Thébaud lab

@LabThebaud

5 years

Check out the new preprint manuscript from our lab "Multiplexed single-cell transcriptomic analysis of normal and impaired lung development in the mouse" by @IvanaMizikova and @HurskainenMaria !! @DavidPCook @EmmiHelle @MarkkuHeikinhe1

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David Cook

@DavidPCook

7 years

1) I hate red-green heatmaps. 2) I reaaally hate red-green heatmaps that use red for higher values

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David Cook

@DavidPCook

10 months

@10xGenomics serious respect for the quality of the Xenium Explorer. Such a smooth experience exploring data. Easy to get lost in there for hours!

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David Cook

@DavidPCook

2 years

Excited to see our new opinion article in @trendscancer ! Having struggled to establish unifying molecular principles of EMP in cancer, I've been exploring new conceptual frameworks to help understand its emergence and consequences.

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David Cook

@DavidPCook

4 years

Ooo hello berlin color palette.

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David Cook

@DavidPCook

5 years

Check out MULTI-seq! It’s an incredibly robust and simple approach for multiplexing samples for scRNA-seq. Congrats @cmcginnisUCSF @dpatters10 !!

Nature Methods

@naturemethods

5 years

MULTI-seq enables scRNA-seq sample multiplexing by tagging the cells with lipid-modified oligos.

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David Cook

@DavidPCook

5 years

Pseudotime mountain. Killing a few minutes by playing with Rayshader in R.

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David Cook

@DavidPCook

3 years

Hey single-cell folks. Anyone ever have two similarly sized groups of cells that differ in total UMI counts by large amount (avg 4k vs. 25k) and DGE is largely translation genes higher in group with more UMIs without much else? Weird technical thing? ATAC data doesn't show split

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David Cook

@DavidPCook

3 years

@ItaiYanai I really feel for all the mid-stage grad students that are doing amazing work but start to doubt themselves because they’re losing award competitions to students that maybe fell into a near-complete project and published it. The CV lag is hard for the first 5 years or so.

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David Cook

@DavidPCook

4 years

@sisichen Ooo. This one changed how I thought about cell heterogeneity and single-cell data.

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David Cook

@DavidPCook

2 years

Proud to be a recipient of this award along with some pretty awesome Ontario scientists. Thanks @OICRRisingStars !

Ontario Rising Stars in Cancer Research Network

@OICRRisingStars

2 years

⭐️⭐️⭐️We are pleased to announce the winners of the 2022 OICR Rising Stars Awards⭐️⭐️⭐️ Congratulations to all six awardees this year! Check out more info about them below! Thank you to everyone who applied and we hope to see your application for our next round of awards! (1/6)

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David Cook

@DavidPCook

7 years

Why do my own work when I can spend my day visualizing others’. Force-directed graph of >20k single cells from the recent E8.25 murine embryo paper from the Marioni group. Paper:

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David Cook

@DavidPCook

5 years

Have had a chance to try out bigSCale2 over the last couple months. I've largely been using it for calculating and comparing TF centrality across the regulatory networks it constructs. It's been performing great for me!

Holger Heyn

@hoheyn

5 years

RELEASED! Our updated #SingleCell Analysis Framework #bigSCale2 (). 1. Now in #R 2. Including new feature: Super-clustering 3. New module: Gene Regulatory Network inferrence. 4. Ready-to-use Index Cell (iCell) datasets:

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David Cook

@DavidPCook

6 years

Predicting a cell's future state w/ RNA velocity. Excited to see this finally published! Congrats @GioeleLaManno ! Time for me to learn enough Python to actually use this efficiently 😅.

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David Cook

@DavidPCook

5 years

Is it just me or are JUN/FOS motifs/target always detected as differentially accessible/expressed following treatment?

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David Cook

@DavidPCook

9 months

Check it out this Wednesday from 2-3pm EST! Want to emphasize that this isn't just platform promo/attack. For the sake of our own research, we've been genuinely trying to understand how these platforms perform, where they excel, and where they fall behind.

10x Genomics

@10xGenomics

9 months

#Singlecellspatial imaging technologies empower new insights—but how do the different platforms stack up? Find out in a webinar where leading spatial researchers compared Xenium In Situ and NanoString CosMx and see which came out on top in their hands:

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David Cook

@DavidPCook

5 years

Am I the only one that is visually drawn to dot size more than colour in the default dot plots like this? I find them awfully hard to interpret quickly when the two variables are not correlated.

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David Cook

@DavidPCook

6 years

A jet lag-motivated summary of Day 1 at Single Cell Biology 2018 (Hinxton, UK) #SCB18

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David Cook

@DavidPCook

7 years

I really like this cover...though I may be a bit biased

Nature Portfolio

@NaturePortfolio

7 years

On the cover this week: Single-cell biology. Dissecting life’s mysteries, one cell at a time

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David Cook

@DavidPCook

6 years

Personal site launched at ! Just a fun thing to toy around with. Hope share analyses and thoughts through blog posts and slide decks from talks. First post up: Scanpy, The Mouse Atlas, and Baby Steps Into Python.

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David Cook

@DavidPCook

2 years

@NinaSteele17 @Momademia Our girl went through a phase of having a “witching hour” for a couple hours each night. Perseverance, tagging partner in, along with swaddling, rocking, shushing was our approach. Also had GI issues if put down too soon after feeding. Had to keep her upright for 30mins or so

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David Cook

@DavidPCook

2 years

@tangming2005 @marenbuettner

Introduction to single-cell RNA-seq data analysis in Python using scanpy

This playlist contains all tutorial videos for scanpy. Trainer is Dr. Maren Büttner, Postdoc at the Institute of Computational Biology of the Helmholtz Munic...

www.youtube.com

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David Cook

@DavidPCook

5 years

Flight's booked for Single Cell Genomics Day at @nygenome next week! Looking forward to finally attend. If anyone wants food/beer/coffee, hit me up!

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David Cook

@DavidPCook

5 years

Looking forward to running a day-long scRNA-seq workshop for this. Come visit Ottawa and check it out!

Stem Cell Network

@StemCellNetwork

5 years

The Stem Cell Network and @OIRMnews are pleased to offer the RNA-Seq Analysis workshop once again! Workshop Dates: October 16, 17 & 18, 2019. Application deadline: August 28, 2019. For application & travel award details click here:

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David Cook

@DavidPCook

6 years

Paper for side project recently submitted to 6th journal, and received 11th scholarship rejection over 4 years of grad school today (though I've been lucky to have received an award 3/4 of those years). Learning that coping with rejection is important in science (and hard to do!)

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David Cook

@DavidPCook

6 years

Interesting way to integrate single-cell data from multiple experiments. Seems to perform well - Panoramic stitching of heterogeneous single-cell transcriptomic data

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David Cook

@DavidPCook

4 years

Anyone know of a study that used scRNA-seq to simply compare gene-gene covariance structure across a bunch of different cell types??

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David Cook

@DavidPCook

5 years

If you’re interested in multiplexing scRNA-seq samples (which you should be!), I strongly recommend taking advantage of this. Labeling steps are simple and fast. Happy to share my experience if you have questions!

cmcginnis

@cmcginnis92

5 years

Our bulk MULTI-seq reagent shipment has arrived!!! Order (for free) #singlecell #RNAseq sample multiplexing reagents here --> Less $$$, doublets, and batch effects More samples, perturbations, and replicates #czbiohub #C3STC @dpatters10 @CAT_UCSF

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David Cook

@DavidPCook

7 years

Married this beautiful lady this past weekend. Enjoying relaxing week off in rural Quebec, but stuck with weak beer and scholarship writing

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David Cook

@DavidPCook

6 years

I already forget the paper from a few months ago that first did density plots like this, but I'm loving using them to look at treatment responses in scRNA-seq data

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David Cook

@DavidPCook

4 years

@tangming2005 scattermore seems like a convenient option for this too.

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David Cook

@DavidPCook

3 years

Fun project @lrncarter @bvanderhyden . “Stemness” of simple epithelial cells is discussed a lot, but perturbations that increase it do not promote defined responses and stemness markers are inconsistent. Suspect stemness is a fluffier concept than we give it credit for

Communications Biology

@CommsBio

3 years

@bvanderhyden @DavidPCook @lrncarter et. al identify heterogeneity in the transcriptional profiles of ovarian surface epithelial stem cells induced under different conditions, suggesting transient induction dependent on environmental cues.

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David Cook

@DavidPCook

7 years

Drove some samples from Ottawa to Montreal to meet this little guy. Glad to say our first @10xgenomics run went very smoothly!

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David Cook

@DavidPCook

1 year

@Sanbomics @scverse_team Definitely useful. Appreciate Seurat’s shuffle=T for convenience. Feel like reproducible shuffling would be a sensible default actually

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David Cook

@DavidPCook

7 years

Looking forward to sharing some work on using scRNA-Seq to map the transcriptional manifold of the EMT in ovarian cancer!

Caroline Vergette

@cvergette

7 years

10X Genomics Single Cell Analysis Facility is opening soon at OHRI! Looking forward to the Opening Seminar with Speaker David Cook: @10xgenomics @DavidPCook @TLROttawa #SingleCell @Eventbrite

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David Cook

@DavidPCook

6 years

Fig 1c: PCA coloured by treatment Fig 2a: Same PCA coloured by cluster Reviewer: "Although you used clustered the data, they look very much like the PCA in Fig 1". Me: ...

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David Cook

@DavidPCook

6 years

@arjunrajlab Sure thing! Just pushed them to

GitHub - dpcook/vector_models: vector graphics - feel free to use

vector graphics - feel free to use. Contribute to dpcook/vector_models development by creating an account on GitHub.

github.com

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David Cook

@DavidPCook

7 years

@uOttawaBMI @lisadambrosio2 Mireille has been a big part of the uOttawa research community since I started as a summer student over 4 years ago. Great to see her join the faculty. Looking forward to seeing her program develop!

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David Cook

@DavidPCook

3 years

@rmassonix @Sc_Ninjas Oh interesting! Didn’t know this existed. Wonder how it works under the hood. I always subsetted the data and reprocessed because I figured there was value in defining cluster-specific variable genes, re-running PCA on those, and using that for clustering.

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David Cook

@DavidPCook

6 years

MULTI-seq - Lipid anchored indices for fast, non-perturbative multiplexing of scRNA-seq samples. I was working on an identical approach, so a little bummed about that, but happy to see the method work so well!

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David Cook

@DavidPCook

7 years

Fantastic review of manifold learning methods and their applications in scRNA-Seq data from the @KrishnaswamyLab .

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David Cook

@DavidPCook

7 years

@melodycoutman 1) Take initiative in steering your own project. I find many students only do what their supervisor wants and quickly become detached from the project and stop enjoying the experience. 2) Network/make friends with other trainees outside your lab. Great for venting & collaboration

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David Cook

@DavidPCook

6 years

Just had a chance to try out Harmony for aligning multiple single-cell datasets. Works remarkably well and is super fast! . >30k cells and ran on laptop in <5mins. Before and After:

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David Cook

@DavidPCook

5 years

At the airport drinking my last cup of Tim Hortons for a week. Excited to head off to the @NatureConf “The Tumour Cell: Plasticity, Progression, and Therapy” in NYC #Tumour19

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David Cook

@DavidPCook

6 years

Oooo I want to use this GIF in presentations

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David Cook

@DavidPCook

4 years

Ooooo yes, this sounds fun

Albert Vilella

@AlbertVilella

4 years

#ChromiumX 1M cells per run experiment. No word on price per bead compared to Chromium NextGEM.

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David Cook

@DavidPCook

5 years

Aw yeah, this is awesome. Combining combinatorial barcoding with droplet methods to get >150k cells per 10x lane.

André Rendeiro

@afrendeiro

5 years

Very excited to share our new preprint describing a method for ultra-high throughput single-cell RNA-seq #scRNAseq

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David Cook

@DavidPCook

6 years

Graph layout of embryonic organ explants from genetic mouse model. Nice reminder that effects of gene/pathway manipulation can be quite variable across a single organ: depletion of one cell type, divergence of two others, and no noticeable effect across the rest

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David Cook

@DavidPCook

6 years

Oh man, this is awesome. Figured it was only a matter of time before ATAC/RNA could be co-assayed at scale

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David Cook

@DavidPCook

6 years

More tools for multiplexing scRNA-seq fom the @lpachter group! Working on a method myself

bioRxiv

@biorxivpreprint

6 years

Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces #bioRxiv

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David Cook

@DavidPCook

2 years

@rmassonix I appreciate and agree with all those points, but I suspect that, for better or worse, many (>50%?) people analyzing and publishing sc data have a casual background in coding at best. As it is now, the python ecosystem is simply too impenetrable to these users.

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David Cook

@DavidPCook

6 years

Ahhhh scATAC-Seq on the 10x is finally coming. #AGBT18 :D :D

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David Cook

@DavidPCook

7 years

All the Vanderhyden grad students in one spot! #OHResDay

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David Cook

@DavidPCook

8 years

Great post by @jtleek on @simplystats discussing modern approaches of publishing for the junior scientist.

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David Cook

@DavidPCook

6 years

Fantastic application of scRNA-seq! Integrating GWAS with cell atlases to infer affected cell types

Jens Hjerling Leffler ⭐️⭐️🇺🇦

@HjerlingLeffler

6 years

It’s finally out! How to use scRNAseq to dissect schizophrenia. Thanks to our great collaborators in the Sullivan lab and others. @n_skene @slinnarsson @PGCgenetics

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David Cook

@DavidPCook

7 years

Been thinking about this one for the last two days. Pretty messed up that the field can sing praise about this work and it gets outright rejected. Can’t believe how happy I am the preprint exists. Running Velocyto as I type

Sten Linnarsson

@slinnarsson

7 years

Reviews back for our RNA velocity paper: only two reviews (?!). One referee calls it ”a transformative contribution to the field”, the other ”very exciting” (but nitpicks about splicing kinetics). Paper rejected outright 😒. WTF.

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David Cook

@DavidPCook

6 years

Nuclei hashing for multiplexing single-nuclei experiments

bioRxiv

@biorxivpreprint

6 years

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics #bioRxiv

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David Cook

@DavidPCook

6 years

Today I learned that some people say "Tiznee plot" instead of "Teesnee plot"

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David Cook

@DavidPCook

7 years

1/n. This is an interesting point. I suspect perceived competition is at the root of many mental health problems in #gradschool

Melissa Cristina Márquez

@mcmsharksxx

7 years

#Gradschool is not a competition. People will try to compete. Do not get sucked into that.

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David Cook

@DavidPCook

6 years

Missed that the date and location had been set for the @10xgenomics User Group Meeting in Toronto. Save the date! June 13, MaRS Discovery District.

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David Cook

@DavidPCook

6 years

There's a clown in my tSNE plot

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David Cook

@DavidPCook

2 years

@cterminiPhD Ooo! a stock of tube racks before they get pilfered and hidden away in students’ drawers! 😲😲

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David Cook

@DavidPCook

7 years

When you wake up early to “be productive” and end up spending 2 hours watching YouTube videos

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David Cook

@DavidPCook

6 years

Any twitter folk going to Single Cell Biology 2018 #SCB2018 in Hinxton next week??? My first single-cell conference 😍

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David Cook

@DavidPCook

9 months

Also, quantifying transcripts per X isn't very informative when the probesets are wildly different. The CosMx panel includes some highly expressed genes that are avoided in the 10x probes. In the CosMx data, MALAT1, XBP1, and TPT1 account for 25% of all transcripts

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David Cook

@DavidPCook

6 years

Excited to see Mark Lynch from Fluidigm talk about upcoming combined RNA and ATAC-seq! I think he skipped past the data slide though 😩 #SCB18

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David Cook

@DavidPCook

6 years

Spending more time in Python recently, I've really come to appreciate the documentation standards for R packages. sci-kit learn aside, I miss having thorough vignettes

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David Cook

@DavidPCook

6 years

@strnr I’ve been wondering lately about how many of the distinct populations/“cell types” inferred from tSNE are either continuous phenotypes to other populations that get detached by the algorithm or even just artificial breaks in the underlying structure

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