#scrnaseq — Public Fediverse posts

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Aligning #scRNAseq datasets along a shared temporal axis across studies, species & systems is hard. This study uses meta-analytic models to develop a #transcriptomic measure of #neurodevelopmental timing that is applicable to different organisms & tissue types @PLOSBiology https://plos.io/4ch0XiX

Interesting #10XGenomics #Flex #scRNAseq #bias

Original post: https://bsky.app/profile/did:plc:4hfcecqwahpnojy4sr7vay6j/post/3mj4ovdavhs2d

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

#NeuralStemCells (NSCs) & ependymal cells (ECs) are derived from #RadialGlialCells. This study uses #scRNAseq to characterize cell fate trajectories in the developing #VentricularZone, identifying TFEB as a regulator of the NSC/EPC balance @PLOSBiology https://plos.io/3HbrsJG

Pipeline release! nf-core/scnanoseq v1.2.0 - nf-core/scnanoseq v1.2.0 - Copper Rhinoceros!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.0

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

How do #brain cells change over #evolution? @bentonlab compare #scRNAseq from ecologically distinct #drosophilid species to identify changes in composition & gene expression of different cell types, revealing higher divergence in #glia than #neurons @PLOSBiology https://plos.io/4js7Rms

How does transcriptional patterning regulate #SalivaryGland #morphogenesis? Annabel May & @katjaroeper use #scRNAseq of early morphogenesis of the #Drosophila salivary gland placode to reveal regulation by induction & exclusion of regulatory factors @PLOSBiology https://plos.io/4cUw827

Pipeline release! nf-core/scnanoseq v1.1.0 - nf-core/scnanoseq v1.1.0 - Iron Alligator!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.1.0

#10xgenomics #longreadsequencing #nanopore #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Uneven #hormone distribution in #plants regulates #cell_division and #growth, biologists discover.

#Brassinosteroids #signalling #cell_cycle #agriculture #scRNAseq

https://phys.org/news/2025-03-uneven-hormone-cell-division-growth.html

2D embeddings for high-dimensional data, the battle rages on

#umap #tsne #scrnaseq

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012403

Coming to #biocuration2025? Join our workshop scFAIR: FAIRification of single-cell data https://www.stowers.org/events/biocuration2025 @SIB @biocurator @marcrr @fbastian
#scRNAseq #FAIR #biocuration #bgee #FAIRdata #FAIRification #scFAIR #SingleCellAnalysis https://sc-fair.org/

Do 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. https://pachterlab.github.io/gget/en/bgee.html #RNAseq #biocuration #Python #scRNAseq @SIB @marcrr @fbastian @dee_unil

#bgee #Bioinformatics #RNASequencing #SingleCellRNASeq #Genomics #Transcriptomics #GeneExpression #ComputationalBiology #SingleCellAnalysis #GeneExpressionAnalysis

"By using time-resolved analyses of scRNA-seq data, we determined the potential transitional trajectories of tumor cells and identified the metastasis-initiating subpopulations"

https://link.springer.com/article/10.1007/s11684-024-1081-7

Reading right now. The identification of cells that initiate #metastasis are of interest, although n=2 paired primary and #BoneMarrow samples may be a bit limited.

#scRNAseq #tumour #Neuroblastoma #pseudotime

Has anyone got references (or ideas/recommendations) for how to perform #data #augmentation on #scrnaseq data (to use in training #ann)?

This is the only paper I could find, but maybe I am not searching for the right thing...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592700/

#machinelearnig #biology

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

Bgee has a new look! We have officially switched to the new Bgee website. Check us out at https://www.bgee.org/ @SIB #scRNAseq #RNAseq #singlecell #GeneExpression #bgee #biocuration #bioinformatics

" The insights derived from this analysis do not only support a CD19 CAR T cell-mediated reset of the memory B cell compartment, but also the parallel inhibition of the interferon signature
in #monocytes and #Tcells of #SLE patients"

https://insight.jci.org/articles/view/179433

Striking that this apparently works better in getting rid of certain memory #Bcells than anti-CD20 antibodies.

#scRNAseq #TCR #carTcells #OpenAccess #science

Surprised to see @Bioconductor methods missing from this #bioinformatics preprint comparing #Seurat and #scanpy for #scRNAseq. Not even a mention that Bioconductor is popular to analyze single cell data. Sometimes it is amazing what a company (10x genomics) recommending a OSS software can do to a community: https://www.biorxiv.org/content/10.1101/2024.04.04.588111v1

Pi-seq: A customizable #OpenSource #multichannel #syringe #pump for #microfluidics:

-no backflow
-#RaspberryPi/#Python-control
-#3Dprinted parts
-cost < 600€
-#Peltier temp. control
-integration in #droplet #scRNAseq

https://doi.org/10.1016/j.ohx.2024.e00517
#DIYbio #lab #instruments #fluidics

Pi-seq: A customizable #OpenSource #multichannel #syringe #pump for #microfluidics:

-no backflow
-#RaspberryPi/#Python-control
-#3Dprinted parts
-cost < 600€
-#Peltier temp. control
-integration in #droplet #scRNAseq

https://doi.org/10.1016/j.ohx.2024.e00517
#DIYbio #lab #instruments #fluidics

Pi-seq: A customizable #OpenSource #multichannel #syringe #pump for #microfluidics:

-no backflow
-#RaspberryPi/#Python-control
-#3Dprinted parts
-cost < 600€
-#Peltier temp. control
-integration in #droplet #scRNAseq

https://doi.org/10.1016/j.ohx.2024.e00517
#DIYbio #lab #instruments #fluidics

Pi-seq: A customizable #OpenSource #multichannel #syringe #pump for #microfluidics:

-no backflow
-#RaspberryPi/#Python-control
-#3Dprinted parts
-cost < 600€
-#Peltier temp. control
-integration in #droplet #scRNAseq

https://doi.org/10.1016/j.ohx.2024.e00517
#DIYbio #lab #instruments #fluidics

Pi-seq: A customizable #OpenSource #multichannel #syringe #pump for #microfluidics:

-no backflow
-#RaspberryPi/#Python-control
-#3Dprinted parts
-cost < 600€
-#Peltier temp. control
-integration in #droplet #scRNAseq

https://doi.org/10.1016/j.ohx.2024.e00517
#DIYbio #lab #instruments #fluidics

#AlternativeSplicing during development. #scRNAseq of mouse #oocyte to #blastocyst reveals large-scale isoform switching & #TransposableElement regulation during the maternal-to-zygotic gene transition #PLOSBiology https://plos.io/4bBFFu1

@foaylward .mtx files are read by Matrix but @bioconductor has great packages and pipelines to analyse #single_cell and #scRNAseq data.

Excited to share a new #preprint! This represents a truly gargantuan effort to profile #ImmuneCells across the human body as part of the #HumanCellAtlas network. Using multimodal profiling of single cells, we uncover tissue-directed and age-associated gene and protein signatures, which will help us understand features of healthy immune cell heterogenity across life!

https://www.biorxiv.org/content/10.1101/2024.01.03.573877v2.full

#scRNAseq #CITEseq #Multiomics #Immunology #TissueImmunity #Research

🧵1/7

I made a short video of the strange things UMAP and t-SNE can do to your data. The algorithms are shown mostly working as intended, yet with some surprising consequences.

#umap #tsne #scrnaseq #wtf

https://www.youtube.com/watch?v=gwqU9OoFwjQ

Macrophages are essential immune cells that reside in all tissues. Some macrophages arise from monocytes in the blood, but during fetal development they also come from a unique pathway!

We still have a lot to learn, but here I'll describe how Zhao et al. (2023) used mouse models to uncover hints about which progenitor cells create tissue-macrophages.

https://doi.org/10.1016/j.celrep.2023.113364

#Macrophages #MouseModel #Immunology #Immunity #scRNAseq #FlowCytometry #Research #JournalArticle #JournalClub

1/9🧵

Hello #scrnaseq wizards out there! Anyone can help answer this question?
https://www.biostars.org/p/9578398/

I'm happy with the #Seurat + #Signac pipeline but I'm not sure what to do and how to merge the two sets of data (#multiomics and #scRNAseq)

#bioinformatics

Great insights from Lior Pachter's computational biology class at Caltech! Check it out: https://t.co/4XVHwEZpZV. Topics selected have relevance in >=3 bio areas, with examples specifically from #scRNAseq. Homework blends theory with hands-on data exploration via #GoogleColab.

Marius Lange #BC2basel: increasing complexity of #SingleCell data leads to problems of temporal, spatial and spatio-temporal mapping. The solution proposed is optimal transport applications, implemented in Moscot:
https://moscot.readthedocs.io/en/latest/
https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2 #SpatialTranscriptomics #scRNAseq

Excellent conclusions of Jean Fan #BC2basel on #machinelearning applied to #scRNAseq #SpatialTranscriptomics