scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.

Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li

May 2021 Genome Biol

Synopsis of Social media discussions

The discussions surrounding the publication often mention scDesign2’s ability to maintain gene correlations and generate high-fidelity data, with comments emphasizing its relevance in fields like data science and bioinformatics. Phrases such as 'transformative tool' and mentions of its probabilistic model suggest that many users are not only aware of scDesign2's capabilities but see it as a significant innovation in the field, which contributes to the overall positive sentiment.

A
Agreement
 Moderate agreement

Most discussions reflect a supportive stance towards scDesign2, with several users highlighting its innovative features.

I
Interest
 High level of interest

There is strong curiosity about the capabilities of scDesign2, evidenced by multiple users engaging with aspects of the simulator.

E
Engagement
 High engagement

Discussions delve into specific technical features, such as the use of copulas, indicating a deeper understanding and connection to the topic.

I
Impact
 High level of impact

Participants perceive this simulator as having significant potential to advance research in single-cell transcriptomics.

Social Mentions

YouTube

2 Videos

Twitter

76 Posts

Metrics

Video Views

1,722

Total Likes

143

Extended Reach

610,623

Social Features

78

Timeline: Posts about article

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  • Daniel Osorio
    @dcosorioh (Twitter)

    @mo_lotfollahi If you have a reference dataset with the cell types you are interested in, you may use scDesign2 https://t.co/KQ2rP5jUEN
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    January 10, 2024

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  • Jingyi Jessica Li (李婧翌)
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  • Single Cell Media
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  • Genome Biology
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  • Jingyi Jessica Li (李婧翌)
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    Our simulator scDesign2 developed by @TianyiSun17 is published at @GenomeBiology. It uses a copula-based probabilistic model to generate realistic single-cell gene counts, preserves gene correlations, and allows user-specified seq depth and cell number. https://t.co/mIVLieSWqx
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Abstract Synopsis

  • scDesign2 is a new simulator designed to create realistic single-cell gene expression data while preserving gene correlations.
  • It addresses key challenges in single-cell transcriptomics by meeting three objectives: maintaining gene integrity, capturing correlations, and generating variable cell counts.
  • The simulator employs probabilistic models and utilizes copulas to enhance its transparency and precision in generating high-quality synthetic data.