The shaky foundations of simulating single-cell RNA sequencing data.

Helena L Crowell, Sarah X Morillo Leonardo, Charlotte Soneson, Mark D Robinson

March 2023 Genome Biol

Synopsis of Social media discussions

Many posts refer to the shaky foundation of single-cell RNA sequencing data simulation, with phrases like 'built on sand' suggesting foundational issues in the methodology. The tone is both critical and intrigued, as seen in users expressing skepticism about the efficacy of these methods and emphasizing the necessity for further research, contributing to an overall sentiment that the publication could have significant implications for the field.

A
Agreement
 Moderate agreement

Several discussions indicate a shared skepticism towards current methods of simulating single-cell RNA sequencing data, suggesting a general agreement on the issues raised in the publication.

I
Interest
 High level of interest

There is a high level of curiosity shown in the posts, with users expressing a desire to understand and critique the findings.

E
Engagement
 Moderate level of engagement

While many posts simply reference the publication, some users engage more deeply with the implications and methodologies, suggesting a moderate level of engagement.

I
Impact
 High level of impact

The discussions reflect a strong belief that the publication could significantly influence future research in bioinformatics.

Social Mentions

YouTube

1 Videos

Twitter

89 Posts

Blogs

2 Articles

Metrics

Video Views

153

Total Likes

265

Extended Reach

705,488

Social Features

92

Timeline: Posts about article

Top Social Media Posts

Posts referencing the article

Evaluating the Performance of Synthetic scRNA-seq Data Generation

Evaluating the Performance of Synthetic scRNA-seq Data Generation

This study assesses synthetic scRNA-seq data generation methods, focusing on their capability to accurately replicate experimental data. We analyze gene and cell quality controls, revealing that many simulators may provide misleading evaluations regarding integration performance and clustering methods.

Social RTCL TV

July 20, 2023

153 views

  • Yang Fang
    @xiaoxiaoyangs (Twitter)

    RT @BioDecoded: The shaky foundations of simulating single-cell RNA sequencing data | Genome Biology https://t.co/OIuugkau3Q #Bioinformati…
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    April 24, 2023

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  • Haruka Ozaki (尾崎遼)
    @yuifu (Twitter)

    RT @BioDecoded: The shaky foundations of simulating single-cell RNA sequencing data | Genome Biology https://t.co/OIuugkau3Q #Bioinformati…
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    April 24, 2023

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  • Seungho Oh @seunghooh@genomic.social
    @dancewithsun (Twitter)

    RT @BioDecoded: The shaky foundations of simulating single-cell RNA sequencing data | Genome Biology https://t.co/OIuugkau3Q #Bioinformati…
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    April 24, 2023

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  • BioDecoded
    @BioDecoded (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data | Genome Biology https://t.co/OIuugkau3Q #Bioinformatics https://t.co/GXYICEE3Jy
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    April 24, 2023

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  • Kelly A. Hogan Ph.D.
    @Loose_Lab_Rat (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data https://t.co/9JpqkHTHss
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    April 4, 2023

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  • Helena Lucia Crowell
    @helucro (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 3, 2023

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  • Jovana Maksimovic
    @JovMaksimovic (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 3, 2023

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  • Mark R@markrobinsonca@{genomic.social,bsky.social}
    @markrobinsonca (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 3, 2023

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  • MADscientist
    @madscientist190 (Twitter)

    RT @DrDx11696608: The shaky foundations of simulating single-cell RNA sequencing data https://t.co/OArYe8p6wW #single #cell #RNA #Bioinform…
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    April 2, 2023

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  • Matt Ritchie
    @mritchieau (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Bioinformatics Trends 
    @BinfoTrends (Twitter)

    RT @DrDx11696608: The shaky foundations of simulating single-cell RNA sequencing data https://t.co/OArYe8p6wW #single #cell #RNA #Bioinform…
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    April 2, 2023

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  • IBE
    @DrDx11696608 (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data https://t.co/OArYe8p6wW #single #cell #RNA #Bioinformatics https://t.co/Bz9WeX6XAD
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  • Yamauchi Yuhei　山内悠平
    @TheoBioYuhei (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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  • ZheFrench
    @ZheFrench (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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  • Ron Finn
    @Finnsense (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Domenico Bellomo
    @BellomoDomenico (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Lindsay K Pino - @lkpino@genomic.social
    @lkpino (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Arthur Liberzon
    @arthlib (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Pau Badia i Mompel
    @PauBadiaM (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • KirinRan
    @NewKirinRanChan (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Ernesto Paas
    @netoelgrande (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • subho
    @subhobrata1 (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Noor Pratap Singh
    @PratapNoor (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 2, 2023

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  • Dr. Günaşık
    @MrsZngn (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • priya joseph
    @ayirpelle (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • Kyle Tretina, Ph.D.
    @AllThingsApx (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • kspt
    @jimin926 (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • Joseph D. Janizek
    @joejanizek (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • Peter
    @BiotechPedro (Twitter)

    RT @jmschreiber91: I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exact…
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    April 1, 2023

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  • Jacob Schreiber
    @jmschreiber91 (Twitter)

    I was always skeptical of single-cell data simulation methods because we still have lingering questions about what exactly the readout is (e.g., it's not a uniform sampling of active genes in a cell). Good to see work on it. https://t.co/bArGPSli3p
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  • single cell papers
    @sc_papers (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data https://t.co/FI1UMEQLFj https://t.co/ydiy7xXLGv
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    March 30, 2023

  • CompBiolPapers
    @CompBiolPapers (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data https://t.co/bXI81yY1Cu
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    March 30, 2023

  • Bioinformatics Trends 
    @BinfoTrends (Twitter)

    RT @jsantoyo: The shaky foundations of simulating single-cell RNA sequencing data. #SingleCell #scRNAseq #SimulatedData @GenomeBiology htt…
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    March 29, 2023

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  • Javier Santoyo
    @jsantoyo (Twitter)

    The shaky foundations of simulating single-cell RNA sequencing data. #SingleCell #scRNAseq #SimulatedData @GenomeBiology https://t.co/cC960SQ7kH
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    March 29, 2023

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  • The Innovation | Medicine
    @Innov_Medicine (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 22, 2022

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  • Kai Xu
    @sdxk163 (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 17, 2022

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  • Jeanne Bark
    @marc_herb (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 17, 2022

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  • Hamim Zafar
    @Quasarzafar (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 16, 2022

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  • Rintu Kutum
    @rintukutum (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 16, 2022

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  • Davide Cirillo
    @Davide__Cirillo (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Seyoon Lee
    @Seyoon_L (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Will Macnair
    @willmacnair (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • aln
    @systemnaBio (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Bodhi Dharma
    @dharma92biol (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Yi-Wen Hsiao
    @YWHSIAO9419 (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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    August 16, 2022

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  • Nancy Yu
    @ynancy (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Paul Geeleher
    @PGeeleher (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYt…
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  • Stephen Turner
    @strnr (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/Sm6v7VxxVZ https://t.co/pqOFxYYtfh
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  • Taco Jesse
    @TJesse62 (Twitter)

    RT @jsantoyo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data. #scRNAseq #DataSimulation https://t.co/BJ…
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    March 1, 2022

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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @jsantoyo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data. #scRNAseq #DataSimulation https://t.co/BJ…
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  • Bioinformatics Trends 
    @BinfoTrends (Twitter)

    RT @jsantoyo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data. #scRNAseq #DataSimulation https://t.co/BJ…
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  • Javier Santoyo
    @jsantoyo (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data. #scRNAseq #DataSimulation https://t.co/BJbeIAtHgP @biorxivpreprint
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    March 1, 2022

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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @CompBiolPapers: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data [NEW RESULTS] https://t.co/ehGr2fCfF1
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    January 30, 2022

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  • CompBiolPapers
    @CompBiolPapers (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data [NEW RESULTS] https://t.co/ehGr2fCfF1
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  • Michael P.H. Stumpf
    @theosysbio (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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    November 17, 2021

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  • PromisingPreprints
    @PromPreprint (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/87iiUzJS5e
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    November 17, 2021

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  • Holger Heyn
    @hoheyn (Twitter)

    CONGRATS @CrowellHL and @markrobinsonca. #singlecell simulation tools benchmarked. Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/ec1VLt1PZs
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    November 17, 2021

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  • archieyoung
    @archieyoung14 (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • D. Zambrana
    @mz_deyvis (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Aaron Kwok
    @aaronkwc (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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  • Florian Vasilescu
    @singlecellgenie (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Prasath Lab CCHMC
    @PrasathLab (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Helena Lucia Crowell
    @helucro (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Chris Ghadban
    @ceghadban (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Rintu Kutum
    @rintukutum (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Anshul Kundaje (anshulkundaje@bluesky)
    @anshulkundaje (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Petar
    @pvtodorov (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Jeroen Gilis
    @GilisJeroen (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Mark R@markrobinsonca@{genomic.social,bsky.social}
    @markrobinsonca (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • ZDQ&Interlaken
    @ZDQ_Interlaken (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Mick W@tson ↙️
    @BioMickWatson (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Sean Simmons
    @seankenneths (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • WeiTing Lin(GR15
    @weitinglin66 (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • @nomad421 (Twitter)

    RT @strnr: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap…
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  • Stephen Turner
    @strnr (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/BHUF9qTR7T https://t.co/Qkn7dUap7J https://t.co/GQXvfEr35Q
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  • antisense.
    @razoralign (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/8tDyeT07L1 https://t.co/Pvj4UV30gf
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  • Helio Rocha
    @_elioRocha (Twitter)

    #bioRxiv Built on sand: the shaky foundations of simulating single-cell RNA sequencing data #bioinfo https://t.co/d6rqI4v0bb
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  • Alan Murphy
    @Al_Murphy_ (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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  • Peter Hickey
    @PeteHaitch (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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    November 15, 2021

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  • Valentine Svensson
    @vallens (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @biorxiv_bioinfo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/ndf5o77yN0 #biorxiv_b…
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  • Single Cell Media
    @SingleCellMedia (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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  • Matt Challacombe
    @MattChallacombe (Twitter)

    RT @biorxiv_bioinfo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/ndf5o77yN0 #biorxiv_b…
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  • Valan
    @valanvir (Twitter)

    RT @biorxivpreprint: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/rofjNvGcQw #bioRxiv
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  • Aaron Day-Williams
    @AGDAYWILL (Twitter)

    RT @biorxiv_bioinfo: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/ndf5o77yN0 #biorxiv_b…
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  • bioRxiv Bioinfo
    @biorxiv_bioinfo (Twitter)

    Built on sand: the shaky foundations of simulating single-cell RNA sequencing data https://t.co/ndf5o77yN0 #biorxiv_bioinfo
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Abstract Synopsis

  • The rise of single-cell RNA-sequencing (scRNA-seq) datasets has led to many new computational tools, prompting the need for benchmark studies to evaluate the performance of these methods compared to existing ones.
  • This study focuses on assessing synthetic scRNA-seq data generation methods to see how well they replicate actual experimental data, analyzing both gene and cell quality controls and their effects on clustering and batch correction comparisons.
  • Findings indicate that many simulators struggle with complex designs, often giving overly positive evaluations of integration performance and leading to uncertain conclusions about the effectiveness of different clustering methods.