#scrnaseq — Public Fediverse posts

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

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

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 v1.2.1 - 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 v1.2.0 - 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

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

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

"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

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

How does exposure to non-mutagenic environmental factors during development contribute to cancer risk? #scRNAseq & spatial transcriptomics reveal how #EndocrineDisruption of #endometrial cell differentiation by #diethylstilbestrol alters the characteristics of stem & progenitor cells, leading to #cancer development. @WilliamsRepro #PLOSBiology https://plos.io/3QpjazO

" Instead, #Hepatoblastoma #tumors contain a large suppressive #myeloid compartment which poses opportunities for targeting. Specifically, therapeutic antibodies
targeting the #tumor antigen #GPC3 to induce ADCP by #macrophages, in combination with myeloid
#ImmuneCheckpointBlockade (#CD47/SIRPa, or VISTA) could be a feasible strategy to explore in future studies"

Krijgsman et al. from Vercoulen lab in the #UMCUtrecht, on #bioRXiv:
https://www.biorxiv.org/content/10.1101/2023.06.28.546852v1

#scRNAseq #spatial #CyTOF #immunology