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Daniel Hoffmann🌻Single cell RNA-sequencing (<a href="https://mathstodon.xyz/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a>) is an essential method to learn about cells in health and disease. Here we have studied "multiplets", an important source of error of scRNAseq. We find that multiplets are astonishingly frequent and hard to eliminate. <a href="https://doi.org/10.1101/2025.06.09.658708" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1101/2025.06.09.658708</a>

nf-corePipeline release! nf-core/scnanoseq v1.2.0 - nf-core/scnanoseq v1.2.0 - Copper Rhinoceros!Please see the changelog: <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.2.0" rel="nofollow noopener" translate="no" target="_blank">https://github.com/nf-core/scnanoseq/releases/tag/1.2.0</a><a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#10xgenomics</a> <a href="https://mstdn.science/tags/longreadsequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#longreadsequencing</a> <a href="https://mstdn.science/tags/nanopore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nanopore</a> <a href="https://mstdn.science/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener" target="_blank">#singlecell</a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener" target="_blank">#nextflow</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

PLOS BiologyHow do <a href="https://fediscience.org/tags/brain" class="mention hashtag" rel="nofollow noopener" target="_blank">#brain</a> cells change over <a href="https://fediscience.org/tags/evolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#evolution</a>? <a href="https://mstdn.science/@bentonlab" class="u-url mention" rel="nofollow noopener" target="_blank">@bentonlab</a> compare <a href="https://fediscience.org/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> from ecologically distinct <a href="https://fediscience.org/tags/drosophilid" class="mention hashtag" rel="nofollow noopener" target="_blank">#drosophilid</a> species to identify changes in composition & gene expression of different cell types, revealing higher divergence in <a href="https://fediscience.org/tags/glia" class="mention hashtag" rel="nofollow noopener" target="_blank">#glia</a> than <a href="https://fediscience.org/tags/neurons" class="mention hashtag" rel="nofollow noopener" target="_blank">#neurons</a> <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4js7Rms" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/4js7Rms</a>

PLOS BiologyHow does transcriptional patterning regulate <a href="https://fediscience.org/tags/SalivaryGland" class="mention hashtag" rel="nofollow noopener" target="_blank">#SalivaryGland</a> <a href="https://fediscience.org/tags/morphogenesis" class="mention hashtag" rel="nofollow noopener" target="_blank">#morphogenesis</a>? Annabel May & <a href="https://bird.makeup/users/katjaroeper" class="u-url mention" rel="nofollow noopener" target="_blank">@katjaroeper</a> use <a href="https://fediscience.org/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> of early morphogenesis of the <a href="https://fediscience.org/tags/Drosophila" class="mention hashtag" rel="nofollow noopener" target="_blank">#Drosophila</a> salivary gland placode to reveal regulation by induction & exclusion of regulatory factors <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4cUw827" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/4cUw827</a>

Nicola RomanòOur new preprint is now out! Dynamic transcriptional heterogeneity in pituitary corticotrophs<a href="https://www.biorxiv.org/content/10.1101/2025.04.04.645979v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2025.04.04.645979v1</a>We analysed publicly available single-cell RNA sequencing data of pituitary gland tissue and looked at corticotrophs, cells that are central to mediate stress responses.We identified several transcriptional states in these cells that are related to how they respond to stress. Cells are able to transition between these states and this might be helpful for them to respond to stress coming at unpredictable times.We also highlight issues related to using scRNAseq to look at functional subpopulations of cells.<a href="https://qoto.org/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> <a href="https://qoto.org/tags/stress" class="mention hashtag" rel="nofollow noopener" target="_blank">#stress</a> <a href="https://qoto.org/tags/physiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#physiology</a> <a href="https://qoto.org/tags/cellbiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#cellbiology</a> <a href="https://qoto.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://qoto.org/tags/corticotrophs" class="mention hashtag" rel="nofollow noopener" target="_blank">#corticotrophs</a> <a href="https://qoto.org/tags/pituitary" class="mention hashtag" rel="nofollow noopener" target="_blank">#pituitary</a>

nf-corePipeline release! nf-core/scnanoseq v1.1.0 - nf-core/scnanoseq v1.1.0 - Iron Alligator!Please see the changelog: <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.1.0" rel="nofollow noopener" translate="no" target="_blank">https://github.com/nf-core/scnanoseq/releases/tag/1.1.0</a><a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#10xgenomics</a> <a href="https://mstdn.science/tags/longreadsequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#longreadsequencing</a> <a href="https://mstdn.science/tags/nanopore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nanopore</a> <a href="https://mstdn.science/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener" target="_blank">#singlecell</a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener" target="_blank">#nextflow</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

CellBioNewsUneven <a href="https://scientificnetwork.de/tags/hormone" class="mention hashtag" rel="nofollow noopener" target="_blank">#hormone</a> distribution in <a href="https://scientificnetwork.de/tags/plants" class="mention hashtag" rel="nofollow noopener" target="_blank">#plants</a> regulates <a href="https://scientificnetwork.de/tags/cell_division" class="mention hashtag" rel="nofollow noopener" target="_blank">#cell_division</a> and <a href="https://scientificnetwork.de/tags/growth" class="mention hashtag" rel="nofollow noopener" target="_blank">#growth</a>, biologists discover.<a href="https://scientificnetwork.de/tags/Brassinosteroids" class="mention hashtag" rel="nofollow noopener" target="_blank">#Brassinosteroids</a> <a href="https://scientificnetwork.de/tags/signalling" class="mention hashtag" rel="nofollow noopener" target="_blank">#signalling</a> <a href="https://scientificnetwork.de/tags/cell_cycle" class="mention hashtag" rel="nofollow noopener" target="_blank">#cell_cycle</a> <a href="https://scientificnetwork.de/tags/agriculture" class="mention hashtag" rel="nofollow noopener" target="_blank">#agriculture</a> <a href="https://scientificnetwork.de/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://phys.org/news/2025-03-uneven-hormone-cell-division-growth.html" rel="nofollow noopener" translate="no" target="_blank">https://phys.org/news/2025-03-uneven-hormone-cell-division-growth.html</a>

Ming 'Tommy' Tangmascarade package implements a procedure to automatically generate 2D masks for clusters on single-cell dimensional reduction plots like t-SNE or UMAP <a href="https://github.com/alserglab/mascarade" rel="nofollow noopener" translate="no" target="_blank">https://github.com/alserglab/mascarade</a> <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a>

Ming 'Tommy' Tangchatomics! How to Fine-Tune the Best Clustering Resolution for <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> Data 🎯 🧵

Dom SommaFinally, our paper studying synovial tissue <a href="https://genomic.social/tags/DC" class="mention hashtag" rel="nofollow noopener" target="_blank">#DC</a> <a href="https://genomic.social/tags/DendtriticCells" class="mention hashtag" rel="nofollow noopener" target="_blank">#DendtriticCells</a> in joint health and <a href="https://genomic.social/tags/rheumatoidArthritis" class="mention hashtag" rel="nofollow noopener" target="_blank">#rheumatoidArthritis</a> is out in Immunity! <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://genomic.social/tags/spatialTranscriptomic" class="mention hashtag" rel="nofollow noopener" target="_blank">#spatialTranscriptomic</a> From: <a href="https://mstdn.science/@ImmunityCP" class="u-url mention" rel="nofollow noopener" target="_blank">@ImmunityCP</a> <a href="https://mstdn.science/@ImmunityCP/113557582489769767" rel="nofollow noopener" translate="no" target="_blank">https://mstdn.science/@ImmunityCP/113557582489769767</a>

LaborjournalInsbesondere bei der Interpretation von <a href="https://mstdn.science/tags/RNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#RNA</a>-Sequenzanalysen einzelner Zellen (<a href="https://mstdn.science/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a>) sind Techniken zur Dimensionen-Reduktion wie <a href="https://mstdn.science/tags/UMAP" class="mention hashtag" rel="nofollow noopener" target="_blank">#UMAP</a> der neuste Schrei. Doch bilden UMAP-Plots tatsächlich die Realität ab? Es gibt Zweifel … Zur Methoden-Kontroverse: <a href="https://www.laborjournal.de/rubric/hintergrund/hg/hg_24_11_01.php" rel="nofollow noopener" translate="no" target="_blank">https://www.laborjournal.de/rubric/hintergrund/hg/hg_24_11_01.php</a>

Bgee databaseComing to <a href="https://genomic.social/tags/biocuration2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#biocuration2025</a>? Join our workshop scFAIR: FAIRification of single-cell data <a href="https://www.stowers.org/events/biocuration2025" rel="nofollow noopener" translate="no" target="_blank">https://www.stowers.org/events/biocuration2025</a> <a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener" target="_blank">@SIB</a> <a href="https://genomic.social/@biocurator" class="u-url mention" rel="nofollow noopener" target="_blank">@biocurator</a> <a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener" target="_blank">@marcrr</a> <a href="https://ecoevo.social/@fbastian" class="u-url mention" rel="nofollow noopener" target="_blank">@fbastian</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://genomic.social/tags/FAIR" class="mention hashtag" rel="nofollow noopener" target="_blank">#FAIR</a> <a href="https://genomic.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener" target="_blank">#biocuration</a> <a href="https://genomic.social/tags/bgee" class="mention hashtag" rel="nofollow noopener" target="_blank">#bgee</a> <a href="https://genomic.social/tags/FAIRdata" class="mention hashtag" rel="nofollow noopener" target="_blank">#FAIRdata</a> <a href="https://genomic.social/tags/FAIRification" class="mention hashtag" rel="nofollow noopener" target="_blank">#FAIRification</a> <a href="https://genomic.social/tags/scFAIR" class="mention hashtag" rel="nofollow noopener" target="_blank">#scFAIR</a> <a href="https://genomic.social/tags/SingleCellAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCellAnalysis</a> <a href="https://sc-fair.org/" rel="nofollow noopener" translate="no" target="_blank">https://sc-fair.org/</a>

Jim RoseIt’s been a while since I’ve had to design a <a href="https://genomic.social/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> pipeline. What tools are folks using for optimizing clustering resolution, or is it all still done iteratively (I.e. by “feel” using bio knowledge) <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/singlecellrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#singlecellrnaseq</a> <a href="https://genomic.social/tags/clustering" class="mention hashtag" rel="nofollow noopener" target="_blank">#clustering</a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a>

Bgee databaseDo you know gget by the Pachter lab? You should! It now includes efficient querying of Bgee in Python. Get high quality curated gene expression data directly in Python or command line. <a href="https://pachterlab.github.io/gget/en/bgee.html" rel="nofollow noopener" translate="no" target="_blank">https://pachterlab.github.io/gget/en/bgee.html</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#RNAseq</a> <a href="https://genomic.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener" target="_blank">#biocuration</a> <a href="https://genomic.social/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener" target="_blank">@SIB</a> <a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener" target="_blank">@marcrr</a> <a href="https://ecoevo.social/@fbastian" class="u-url mention" rel="nofollow noopener" target="_blank">@fbastian</a> <a href="https://ecoevo.social/@dee_unil" class="u-url mention" rel="nofollow noopener" target="_blank">@dee_unil</a><a href="https://genomic.social/tags/bgee" class="mention hashtag" rel="nofollow noopener" target="_blank">#bgee</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/RNASequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#RNASequencing</a> <a href="https://genomic.social/tags/SingleCellRNASeq" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCellRNASeq</a> <a href="https://genomic.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genomics</a> <a href="https://genomic.social/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Transcriptomics</a> <a href="https://genomic.social/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneExpression</a> <a href="https://genomic.social/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> <a href="https://genomic.social/tags/SingleCellAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCellAnalysis</a> <a href="https://genomic.social/tags/GeneExpressionAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneExpressionAnalysis</a>

Dom SommaparaCell: A novel software tool for the interactive analysis and visualization of host-parasite single cell RNA-Seq data (without knowing programming) <a href="https://biorxiv.org/content/10.1101/2024.08.29.610375v1" rel="nofollow noopener" translate="no" target="_blank">https://biorxiv.org/content/10.1101/2024.08.29.610375v1</a> . Interested in the datasets? Here: <a href="http://cellatlas.mvls.gla.ac.uk" rel="nofollow noopener" translate="no" target="_blank">http://cellatlas.mvls.gla.ac.uk</a><a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://genomic.social/tags/parasites" class="mention hashtag" rel="nofollow noopener" target="_blank">#parasites</a>

Arjan Boltjes"By using time-resolved analyses of scRNA-seq data, we determined the potential transitional trajectories of tumor cells and identified the metastasis-initiating subpopulations"<a href="https://link.springer.com/article/10.1007/s11684-024-1081-7" rel="nofollow noopener" translate="no" target="_blank">https://link.springer.com/article/10.1007/s11684-024-1081-7</a>Reading right now. The identification of cells that initiate <a href="https://mastodon.social/tags/metastasis" class="mention hashtag" rel="nofollow noopener" target="_blank">#metastasis</a> are of interest, although n=2 paired primary and <a href="https://mastodon.social/tags/BoneMarrow" class="mention hashtag" rel="nofollow noopener" target="_blank">#BoneMarrow</a> samples may be a bit limited.<a href="https://mastodon.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.social/tags/tumour" class="mention hashtag" rel="nofollow noopener" target="_blank">#tumour</a> <a href="https://mastodon.social/tags/Neuroblastoma" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroblastoma</a> <a href="https://mastodon.social/tags/pseudotime" class="mention hashtag" rel="nofollow noopener" target="_blank">#pseudotime</a>

Thomas SandmannJust read this great paper on "Identifying cell states in single-cell RNA-seq data at statistically maximal resolution" by Pascal Grobecker, Thomas Sakoparnig and Erik van Nimwegen from <a href="https://mstdn.science/@NimwegenLab" class="u-url mention" rel="nofollow noopener" target="_blank">@NimwegenLab</a> They address the issue of ad-hoc clustering of single-cell data by asking "[how can we] maximally reduce the complexity of the dataset without removing any of its meaningful structure"? And then answer it in a rigorous way implemented in {Cellstates}.<a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012224" rel="nofollow noopener" translate="no" target="_blank">https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012224</a>

Nicola RomanòHas anyone got references (or ideas/recommendations) for how to perform <a href="https://qoto.org/tags/data" class="mention hashtag" rel="nofollow noopener" target="_blank">#data</a> <a href="https://qoto.org/tags/augmentation" class="mention hashtag" rel="nofollow noopener" target="_blank">#augmentation</a> on <a href="https://qoto.org/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> data (to use in training <a href="https://qoto.org/tags/ann" class="mention hashtag" rel="nofollow noopener" target="_blank">#ann</a>)?This is the only paper I could find, but maybe I am not searching for the right thing...<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592700/" rel="nofollow noopener" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592700/</a><a href="https://qoto.org/tags/machinelearnig" class="mention hashtag" rel="nofollow noopener" target="_blank">#machinelearnig</a> <a href="https://qoto.org/tags/biology" class="mention hashtag" rel="nofollow noopener" target="_blank">#biology</a>

Nicola RomanòI've been reading again this little gem of a paper <a href="https://diabetesjournals.org/diabetes/article/68/7/1380/39676/Navigating-the-Depths-and-Avoiding-the-Shallows-of" rel="nofollow noopener" target="_blank">https://diabetesjournals.org/diabetes/article/68/7/1380/39676/Navigating-the-Depths-and-Avoiding-the-Shallows-of</a>I'm wondering how many results from <a href="https://qoto.org/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scrnaseq</a> experiments are flawed for the reasons highlighted in there.

Arjan BoltjesOf specific interest for <a href="https://mastodon.social/tags/pediatric" class="mention hashtag" rel="nofollow noopener" target="_blank">#pediatric</a> <a href="https://mastodon.social/tags/cancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#cancer</a> researchers might be the n=4 pediatric healthy control samples included, of which the <a href="https://mastodon.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> according to the statement in the paper is available.<a href="https://mastodon.social/tags/OpenData" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenData</a>

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