Joined May 2017
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- Followers 367
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30 Photos and videos
Igor Dolgalev retweeted
Apr 1
Monthly median Received to Accepted time (days) at Nature Genetics
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Igor Dolgalev retweeted
25 Feb 2025
scBaseCamp was built by directly mining all publicly accessible 10X Genomics scRNAseq data from the Sequence Read Archive (SRA)
With over 230M cells drawn from 21 species, 72 tissues, scBaseCamp is significantly larger and more diverse than existing single-cell data repositories
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13 Jan 2025
Thank you @xuefei_w (@davidvanvalen lab) for a great presentation of DeepCellTypes at our NYU Single-Cell Club. DeepCellTypes is a spatial proteomics phenotyping method with the ability to generalize across diverse datasets with varying marker panels.
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13 Jan 2025
DeepCellTypes pre-print: doi.org/10.1101/2024.11.02.6…
Code and vignettes: vanvalenlab.github.io/deepce…
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Igor Dolgalev retweeted
6 Dec 2024
The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳
For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread.
nature.com/articles/s41592-0…
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Igor Dolgalev retweeted
28 Oct 2024
This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov/
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21 Oct 2024
Thank you @DKotliar (@soumya_boston lab) for a great presentation of CellAnnoTator (*CAT) and T-CellAnnoTator (TCAT) at our NYU Single-Cell Club. TCAT annotates scRNA-Seq T-cell subsets with predefined gene expression programs compiled from a range of reference datasets.
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21 Oct 2024
TCAT pre-print: doi.org/10.1101/2024.05.03.5…
Code and vignettes: github.com/immunogenomics/st…
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Igor Dolgalev retweeted
18 Oct 2024
🗨️ WANNA TALK TO YOUR CELLS? Try out CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conversation. No coding needed, just chat in plain English. Short walkthrough below. Web app & bioRxiv preprint linked in the thread. Let's dive in! (1/9)
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Igor Dolgalev retweeted
4 Oct 2024
Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING!
@10xGenomics @nanostringtech @AkoyaBio @bruker
4 Oct 2024
STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv
@DrJasPlummer @hoheyn @pascual_reguant @eliseinsing @cnag_eu @ACEpigenetics @StJudeResearch biorxiv.org/content/10.1101/…
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Igor Dolgalev retweeted
There's a lot of excitement about foundation models and their ability to learn biology 🧬💻
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
biorxiv.org/content/10.1101/…
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Igor Dolgalev retweeted
24 Jul 2024
Are you missing cells and cell types in your single-cell multiome experiments @10xGenomics? Check out EmptyDropsMultiome @MarioniLab
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Igor Dolgalev retweeted
9 Jul 2024
$ILMN - Illumina buys Fluent Biosciences to accelerate single-cell analysis seekingalpha.com/news/412309…
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Igor Dolgalev retweeted
6 Jul 2024
Systematic comparison of sequencing-based spatial transcriptomic methods in @naturemethods
In summary:
“- Stereo-seq, Slide-tag, Visium shows the better capture efficiency with raw sequencing depth
- Slide-seq V2, Visium (probe), DynaSpatial gives the better capture efficiency with normalized sequencing depth.”
nature.com/articles/s41592-0…
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10 Jun 2024
Thank you @suoqin_jin for a great presentation of CellChat at our NYU Single-Cell Club. CellChat v2 expands the underlying CellChatDB database, extends the inference of cell-cell communication to spatially-resolved datasets, and adds an interactive browser for output exploration.
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10 Jun 2024
CellChat v2 pre-print: doi.org/10.1101/2023.11.05.5…
Code and vignettes: github.com/jinworks/CellChat
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31 May 2024
Seems like you can determine sequencing platform from the quality scores alone using a GPT model open.substack.com/pub/aseq/p…
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Igor Dolgalev retweeted
15 May 2024
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Igor Dolgalev retweeted
14 May 2024
I'm happy to share that out paper on Phantasus, a web-application for visual and interactive gene expression analysis, got out in @eLife elifesciences.org/articles/8… Here, I'm using it to analyze a random GEO dataset, including basic QC to filter outliers, in under 100 seconds! 1/n
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13 May 2024
Thank you @alexlederer19 (@GioeleLaManno lab) for a great presentation of VeloCycle at our NYU Single-Cell Club. VeloCycle is a new implementation of RNA velocity that combines velocity field and manifold estimation, tailored for the cell cycle.
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13 May 2024
VeloCycle pre-print: doi.org/10.1101/2024.01.18.5…
Code and vignettes: github.com/lamanno-epfl/velo…
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